diff --git a/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatForm.svelte b/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatForm.svelte
index f3a8028265..eec90a5d70 100644
--- a/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatForm.svelte
+++ b/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatForm.svelte
@@ -42,6 +42,7 @@
 		onFileUpload?: (files: File[]) => void;
 		onSend?: (message: string, files?: ChatUploadedFile[]) => Promise<boolean>;
 		onStop?: () => void;
+		onSystemPromptAdd?: () => void;
 		showHelperText?: boolean;
 		uploadedFiles?: ChatUploadedFile[];
 	}
@@ -54,6 +55,7 @@
 		onFileUpload,
 		onSend,
 		onStop,
+		onSystemPromptAdd,
 		showHelperText = true,
 		uploadedFiles = $bindable([])
 	}: Props = $props();
@@ -389,6 +391,7 @@
 			onFileUpload={handleFileUpload}
 			onMicClick={handleMicClick}
 			onStop={handleStop}
+			onSystemPromptClick={onSystemPromptAdd}
 		/>
 	</div>
 </form>
diff --git a/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatFormActions/ChatFormActionFileAttachments.svelte b/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatFormActions/ChatFormActionFileAttachments.svelte
index 61bf641aa3..748c55403f 100644
--- a/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatFormActions/ChatFormActionFileAttachments.svelte
+++ b/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatFormActions/ChatFormActionFileAttachments.svelte
@@ -1,5 +1,5 @@
 <script lang="ts">
-	import { Plus } from '@lucide/svelte';
+	import { Plus, MessageSquare } from '@lucide/svelte';
 	import { Button } from '$lib/components/ui/button';
 	import * as DropdownMenu from '$lib/components/ui/dropdown-menu';
 	import * as Tooltip from '$lib/components/ui/tooltip';
@@ -15,6 +15,7 @@
 		showMcpOption?: boolean;
 		onFileUpload?: (fileType?: FileTypeCategory) => void;
 		onMcpClick?: () => void;
+		onSystemPromptClick?: () => void;
 	}
 
 	let {
@@ -24,7 +25,8 @@
 		hasVisionModality = false,
 		showMcpOption = false,
 		onFileUpload,
-		onMcpClick
+		onMcpClick,
+		onSystemPromptClick
 	}: Props = $props();
 
 	const fileUploadTooltipText = 'Add files or MCP servers';
@@ -136,6 +138,24 @@
 					<span>MCP Servers</span>
 				</DropdownMenu.Item>
 			{/if}
+
+			<DropdownMenu.Separator />
+			<Tooltip.Root>
+				<Tooltip.Trigger class="w-full">
+					<DropdownMenu.Item
+						class="flex cursor-pointer items-center gap-2"
+						onclick={() => onSystemPromptClick?.()}
+					>
+						<MessageSquare class="h-4 w-4" />
+
+						<span>System Prompt</span>
+					</DropdownMenu.Item>
+				</Tooltip.Trigger>
+
+				<Tooltip.Content>
+					<p>Add a custom system message for this conversation</p>
+				</Tooltip.Content>
+			</Tooltip.Root>
 		</DropdownMenu.Content>
 	</DropdownMenu.Root>
 </div>
diff --git a/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatFormActions/ChatFormActions.svelte b/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatFormActions/ChatFormActions.svelte
index d6644caaf0..54c8d2a2a8 100644
--- a/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatFormActions/ChatFormActions.svelte
+++ b/tools/server/webui/src/lib/components/app/chat/ChatForm/ChatFormActions/ChatFormActions.svelte
@@ -30,6 +30,7 @@
 		onFileUpload?: (fileType?: FileTypeCategory) => void;
 		onMicClick?: () => void;
 		onStop?: () => void;
+		onSystemPromptClick?: () => void;
 	}
 
 	let {
@@ -42,7 +43,8 @@
 		uploadedFiles = [],
 		onFileUpload,
 		onMicClick,
-		onStop
+		onStop,
+		onSystemPromptClick
 	}: Props = $props();
 
 	let currentConfig = $derived(config());
@@ -167,7 +169,7 @@
 
 	let showMcpDialog = $state(false);
 
-
+	// MCP servers state (simplified - just need to check if any exist)
 	let mcpServers = $derived(parseMcpServerSettings(currentConfig.mcpServers));
 	let hasMcpServers = $derived(mcpServers.length > 0);
 </script>
@@ -181,6 +183,7 @@
 			showMcpOption={!hasMcpServers}
 			onMcpClick={() => (showMcpDialog = true)}
 			{onFileUpload}
+			{onSystemPromptClick}
 		/>
 
 		{#if hasMcpServers}
diff --git a/tools/server/webui/src/lib/components/app/chat/ChatMessages/ChatMessage.svelte b/tools/server/webui/src/lib/components/app/chat/ChatMessages/ChatMessage.svelte
index 9eedf8a4e3..518375582e 100644
--- a/tools/server/webui/src/lib/components/app/chat/ChatMessages/ChatMessage.svelte
+++ b/tools/server/webui/src/lib/components/app/chat/ChatMessages/ChatMessage.svelte
@@ -1,6 +1,15 @@
 <script lang="ts">
-	import { chatStore } from '$lib/stores/chat.svelte';
+	import { goto } from '$app/navigation';
+	import {
+		chatStore,
+		pendingEditMessageId,
+		clearPendingEditMessageId,
+		removeSystemPromptPlaceholder
+	} from '$lib/stores/chat.svelte';
+	import { conversationsStore } from '$lib/stores/conversations.svelte';
+	import { DatabaseService } from '$lib/services';
 	import { config } from '$lib/stores/settings.svelte';
+	import { SYSTEM_MESSAGE_PLACEHOLDER } from '$lib/constants/ui';
 	import { copyToClipboard, isIMEComposing, formatMessageForClipboard } from '$lib/utils';
 	import ChatMessageAssistant from './ChatMessageAssistant.svelte';
 	import ChatMessageUser from './ChatMessageUser.svelte';
@@ -69,8 +78,30 @@
 		return null;
 	});
 
-	function handleCancelEdit() {
+	// Auto-start edit mode if this message is the pending edit target
+	$effect(() => {
+		const pendingId = pendingEditMessageId();
+
+		if (pendingId && pendingId === message.id && !isEditing) {
+			handleEdit();
+			clearPendingEditMessageId();
+		}
+	});
+
+	async function handleCancelEdit() {
 		isEditing = false;
+
+		// If canceling a new system message with placeholder content, remove it without deleting children
+		if (message.role === 'system') {
+			const conversationDeleted = await removeSystemPromptPlaceholder(message.id);
+
+			if (conversationDeleted) {
+				goto('/');
+			}
+
+			return;
+		}
+
 		editedContent = message.content;
 		editedExtras = message.extra ? [...message.extra] : [];
 		editedUploadedFiles = [];
@@ -103,7 +134,12 @@
 
 	function handleEdit() {
 		isEditing = true;
-		editedContent = message.content;
+		// Clear placeholder content for system messages
+		editedContent =
+			message.role === 'system' && message.content === SYSTEM_MESSAGE_PLACEHOLDER
+				? ''
+				: message.content;
+		textareaElement?.focus();
 		editedExtras = message.extra ? [...message.extra] : [];
 		editedUploadedFiles = [];
 
@@ -143,7 +179,26 @@
 	}
 
 	async function handleSaveEdit() {
-		if (message.role === 'user' || message.role === 'system') {
+		if (message.role === 'system') {
+			// System messages: update in place without branching
+			const newContent = editedContent.trim();
+
+			// If content is empty or still the placeholder, remove without deleting children
+			if (!newContent) {
+				const conversationDeleted = await removeSystemPromptPlaceholder(message.id);
+				isEditing = false;
+				if (conversationDeleted) {
+					goto('/');
+				}
+				return;
+			}
+
+			await DatabaseService.updateMessage(message.id, { content: newContent });
+			const index = conversationsStore.findMessageIndex(message.id);
+			if (index !== -1) {
+				conversationsStore.updateMessageAtIndex(index, { content: newContent });
+			}
+		} else if (message.role === 'user') {
 			const finalExtras = await getMergedExtras();
 			onEditWithBranching?.(message, editedContent.trim(), finalExtras);
 		} else {
diff --git a/tools/server/webui/src/lib/components/app/chat/ChatMessages/ChatMessageSystem.svelte b/tools/server/webui/src/lib/components/app/chat/ChatMessages/ChatMessageSystem.svelte
index 269e83776d..4866c3c360 100644
--- a/tools/server/webui/src/lib/components/app/chat/ChatMessages/ChatMessageSystem.svelte
+++ b/tools/server/webui/src/lib/components/app/chat/ChatMessages/ChatMessageSystem.svelte
@@ -116,7 +116,7 @@
 
 				<Button class="h-8 px-3" onclick={onSaveEdit} disabled={!editedContent.trim()} size="sm">
 					<Check class="mr-1 h-3 w-3" />
-					Send
+					Save
 				</Button>
 			</div>
 		</div>
diff --git a/tools/server/webui/src/lib/components/app/chat/ChatScreen/ChatScreen.svelte b/tools/server/webui/src/lib/components/app/chat/ChatScreen/ChatScreen.svelte
index 27439551a1..ed0869f3cc 100644
--- a/tools/server/webui/src/lib/components/app/chat/ChatScreen/ChatScreen.svelte
+++ b/tools/server/webui/src/lib/components/app/chat/ChatScreen/ChatScreen.svelte
@@ -433,6 +433,7 @@
 					onFileUpload={handleFileUpload}
 					onSend={handleSendMessage}
 					onStop={() => chatStore.stopGeneration()}
+					onSystemPromptAdd={() => chatStore.addSystemPrompt()}
 					showHelperText={false}
 					bind:uploadedFiles
 				/>
@@ -491,6 +492,7 @@
 					onFileUpload={handleFileUpload}
 					onSend={handleSendMessage}
 					onStop={() => chatStore.stopGeneration()}
+					onSystemPromptAdd={() => chatStore.addSystemPrompt()}
 					showHelperText={true}
 					bind:uploadedFiles
 				/>
diff --git a/tools/server/webui/src/lib/constants/ui.ts b/tools/server/webui/src/lib/constants/ui.ts
new file mode 100644
index 0000000000..a75b30f2f8
--- /dev/null
+++ b/tools/server/webui/src/lib/constants/ui.ts
@@ -0,0 +1 @@
+export const SYSTEM_MESSAGE_PLACEHOLDER = 'System message';
diff --git a/tools/server/webui/src/lib/stores/chat.svelte.ts b/tools/server/webui/src/lib/stores/chat.svelte.ts
index 03e05c4259..06588dee1e 100644
--- a/tools/server/webui/src/lib/stores/chat.svelte.ts
+++ b/tools/server/webui/src/lib/stores/chat.svelte.ts
@@ -17,6 +17,7 @@ import {
 import { SvelteMap } from 'svelte/reactivity';
 import { DEFAULT_CONTEXT } from '$lib/constants/default-context';
 import { getAgenticConfig } from '$lib/config/agentic';
+import { SYSTEM_MESSAGE_PLACEHOLDER } from '$lib/constants/ui';
 
 /**
  * chatStore - Active AI interaction and streaming state management
@@ -78,6 +79,7 @@ class ChatStore {
 	private isStreamingActive = $state(false);
 	private isEditModeActive = $state(false);
 	private addFilesHandler: ((files: File[]) => void) | null = $state(null);
+	pendingEditMessageId = $state<string | null>(null);
 
 	// ─────────────────────────────────────────────────────────────────────────────
 	// Loading State
@@ -457,6 +459,166 @@ class ChatStore {
 		}
 	}
 
+	/**
+	 * Adds a system message at the top of a conversation and triggers edit mode.
+	 * The system message is inserted between root and the first message of the active branch.
+	 * Creates a new conversation if one doesn't exist.
+	 */
+	async addSystemPrompt(): Promise<void> {
+		let activeConv = conversationsStore.activeConversation;
+
+		// Create conversation if needed
+		if (!activeConv) {
+			await conversationsStore.createConversation();
+			activeConv = conversationsStore.activeConversation;
+		}
+		if (!activeConv) return;
+
+		try {
+			// Get all messages to find the root
+			const allMessages = await conversationsStore.getConversationMessages(activeConv.id);
+			const rootMessage = allMessages.find((m) => m.type === 'root' && m.parent === null);
+			let rootId: string;
+
+			// Create root message if it doesn't exist
+			if (!rootMessage) {
+				rootId = await DatabaseService.createRootMessage(activeConv.id);
+			} else {
+				rootId = rootMessage.id;
+			}
+
+			// Check if there's already a system message as root's child
+			const existingSystemMessage = allMessages.find(
+				(m) => m.role === 'system' && m.parent === rootId
+			);
+
+			if (existingSystemMessage) {
+				// If system message exists, just trigger edit mode on it
+				this.pendingEditMessageId = existingSystemMessage.id;
+
+				// Make sure it's in active messages at the beginning
+				if (!conversationsStore.activeMessages.some((m) => m.id === existingSystemMessage.id)) {
+					conversationsStore.activeMessages.unshift(existingSystemMessage);
+				}
+				return;
+			}
+
+			// Find the first message of the active branch (child of root that's in activeMessages)
+			const activeMessages = conversationsStore.activeMessages;
+			const firstActiveMessage = activeMessages.find((m) => m.parent === rootId);
+
+			// Create new system message with placeholder content (will be edited by user)
+			const systemMessage = await DatabaseService.createSystemMessage(
+				activeConv.id,
+				SYSTEM_MESSAGE_PLACEHOLDER,
+				rootId
+			);
+
+			// If there's a first message in the active branch, re-parent it to the system message
+			if (firstActiveMessage) {
+				// Update the first message's parent to be the system message
+				await DatabaseService.updateMessage(firstActiveMessage.id, {
+					parent: systemMessage.id
+				});
+
+				// Update the system message's children to include the first message
+				await DatabaseService.updateMessage(systemMessage.id, {
+					children: [firstActiveMessage.id]
+				});
+
+				// Remove first message from root's children
+				const updatedRootChildren = rootMessage
+					? rootMessage.children.filter((id: string) => id !== firstActiveMessage.id)
+					: [];
+				// Note: system message was already added to root's children by createSystemMessage
+				await DatabaseService.updateMessage(rootId, {
+					children: [
+						...updatedRootChildren.filter((id: string) => id !== systemMessage.id),
+						systemMessage.id
+					]
+				});
+
+				// Update local state
+				const firstMsgIndex = conversationsStore.findMessageIndex(firstActiveMessage.id);
+				if (firstMsgIndex !== -1) {
+					conversationsStore.updateMessageAtIndex(firstMsgIndex, { parent: systemMessage.id });
+				}
+			}
+
+			// Add system message to active messages at the beginning
+			conversationsStore.activeMessages.unshift(systemMessage);
+
+			// Set pending edit message ID to trigger edit mode
+			this.pendingEditMessageId = systemMessage.id;
+
+			conversationsStore.updateConversationTimestamp();
+		} catch (error) {
+			console.error('Failed to add system prompt:', error);
+		}
+	}
+
+	/**
+	 * Removes a system message placeholder without deleting its children.
+	 * Re-parents children back to the root message.
+	 * If this is a new empty conversation (only root + system placeholder), deletes the entire conversation.
+	 * @returns true if the entire conversation was deleted, false otherwise
+	 */
+	async removeSystemPromptPlaceholder(messageId: string): Promise<boolean> {
+		const activeConv = conversationsStore.activeConversation;
+		if (!activeConv) return false;
+
+		try {
+			const allMessages = await conversationsStore.getConversationMessages(activeConv.id);
+			const systemMessage = allMessages.find((m) => m.id === messageId);
+			if (!systemMessage || systemMessage.role !== 'system') return false;
+
+			const rootMessage = allMessages.find((m) => m.type === 'root' && m.parent === null);
+			if (!rootMessage) return false;
+
+			// Check if this is a new empty conversation (only root + system placeholder)
+			const isEmptyConversation = allMessages.length === 2 && systemMessage.children.length === 0;
+
+			if (isEmptyConversation) {
+				// Delete the entire conversation
+				await conversationsStore.deleteConversation(activeConv.id);
+				return true;
+			}
+
+			// Re-parent system message's children to root
+			for (const childId of systemMessage.children) {
+				await DatabaseService.updateMessage(childId, { parent: rootMessage.id });
+
+				// Update local state
+				const childIndex = conversationsStore.findMessageIndex(childId);
+				if (childIndex !== -1) {
+					conversationsStore.updateMessageAtIndex(childIndex, { parent: rootMessage.id });
+				}
+			}
+
+			// Update root's children: remove system message, add system's children
+			const newRootChildren = [
+				...rootMessage.children.filter((id: string) => id !== messageId),
+				...systemMessage.children
+			];
+			await DatabaseService.updateMessage(rootMessage.id, { children: newRootChildren });
+
+			// Delete the system message (without cascade)
+			await DatabaseService.deleteMessage(messageId);
+
+			// Remove from active messages
+			const systemIndex = conversationsStore.findMessageIndex(messageId);
+			if (systemIndex !== -1) {
+				conversationsStore.activeMessages.splice(systemIndex, 1);
+			}
+
+			conversationsStore.updateConversationTimestamp();
+			return false;
+		} catch (error) {
+			console.error('Failed to remove system prompt placeholder:', error);
+			return false;
+		}
+	}
+
 	private async createAssistantMessage(parentId?: string): Promise<DatabaseMessage | null> {
 		const activeConv = conversationsStore.activeConversation;
 		if (!activeConv) return null;
@@ -1514,3 +1676,7 @@ export const isEditing = () => chatStore.isEditing();
 export const isLoading = () => chatStore.isLoading;
 export const setEditModeActive = (handler: (files: File[]) => void) =>
 	chatStore.setEditModeActive(handler);
+export const pendingEditMessageId = () => chatStore.pendingEditMessageId;
+export const clearPendingEditMessageId = () => (chatStore.pendingEditMessageId = null);
+export const removeSystemPromptPlaceholder = (messageId: string) =>
+	chatStore.removeSystemPromptPlaceholder(messageId);