diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index ad3a064d..381e717d 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 ### Added
 
+- `pi.setLabel(entryId, label)` in ExtensionAPI for setting per-entry labels from extensions ([#806](https://github.com/badlogic/pi-mono/issues/806))
 - Export `keyHint`, `appKeyHint`, `editorKey`, `appKey`, `rawKeyHint` for extensions to format keybinding hints consistently
 - Added `showHardwareCursor` setting to control cursor visibility while still positioning it for IME support. ([#800](https://github.com/badlogic/pi-mono/pull/800) by [@ghoulr](https://github.com/ghoulr))
 - Added `ctx.compact()` and `ctx.getContextUsage()` to extension contexts for programmatic compaction and context usage checks.
diff --git a/packages/coding-agent/docs/extensions.md b/packages/coding-agent/docs/extensions.md
index 75c62cfd..cf62e8ef 100644
--- a/packages/coding-agent/docs/extensions.md
+++ b/packages/coding-agent/docs/extensions.md
@@ -904,6 +904,23 @@ if (name) {
 }
 ```
 
+### pi.setLabel(entryId, label)
+
+Set or clear a label on an entry. Labels are user-defined markers for bookmarking and navigation (shown in `/tree` selector).
+
+```typescript
+// Set a label
+pi.setLabel(entryId, "checkpoint-before-refactor");
+
+// Clear a label
+pi.setLabel(entryId, undefined);
+
+// Read labels via sessionManager
+const label = ctx.sessionManager.getLabel(entryId);
+```
+
+Labels persist in the session and survive restarts. Use them to mark important points (turns, checkpoints) in the conversation tree.
+
 ### pi.registerCommand(name, options)
 
 Register a command.
diff --git a/packages/coding-agent/src/core/extensions/index.ts b/packages/coding-agent/src/core/extensions/index.ts
index 3d487e89..ff81d28e 100644
--- a/packages/coding-agent/src/core/extensions/index.ts
+++ b/packages/coding-agent/src/core/extensions/index.ts
@@ -98,6 +98,7 @@ export type {
 	SessionSwitchEvent,
 	SessionTreeEvent,
 	SetActiveToolsHandler,
+	SetLabelHandler,
 	SetModelHandler,
 	SetThinkingLevelHandler,
 	// Events - Tool
diff --git a/packages/coding-agent/src/core/extensions/loader.ts b/packages/coding-agent/src/core/extensions/loader.ts
index a6bcafda..d15e7e63 100644
--- a/packages/coding-agent/src/core/extensions/loader.ts
+++ b/packages/coding-agent/src/core/extensions/loader.ts
@@ -114,6 +114,7 @@ export function createExtensionRuntime(): ExtensionRuntime {
 		appendEntry: notInitialized,
 		setSessionName: notInitialized,
 		getSessionName: notInitialized,
+		setLabel: notInitialized,
 		getActiveTools: notInitialized,
 		getAllTools: notInitialized,
 		setActiveTools: notInitialized,
@@ -205,6 +206,10 @@ function createExtensionAPI(
 			return runtime.getSessionName();
 		},
 
+		setLabel(entryId: string, label: string | undefined): void {
+			runtime.setLabel(entryId, label);
+		},
+
 		exec(command: string, args: string[], options?: ExecOptions) {
 			return execCommand(command, args, options?.cwd ?? cwd, options);
 		},
diff --git a/packages/coding-agent/src/core/extensions/runner.ts b/packages/coding-agent/src/core/extensions/runner.ts
index 64ffd0b0..4ce99b14 100644
--- a/packages/coding-agent/src/core/extensions/runner.ts
+++ b/packages/coding-agent/src/core/extensions/runner.ts
@@ -149,6 +149,7 @@ export class ExtensionRunner {
 		this.runtime.appendEntry = actions.appendEntry;
 		this.runtime.setSessionName = actions.setSessionName;
 		this.runtime.getSessionName = actions.getSessionName;
+		this.runtime.setLabel = actions.setLabel;
 		this.runtime.getActiveTools = actions.getActiveTools;
 		this.runtime.getAllTools = actions.getAllTools;
 		this.runtime.setActiveTools = actions.setActiveTools;
diff --git a/packages/coding-agent/src/core/extensions/types.ts b/packages/coding-agent/src/core/extensions/types.ts
index a9918344..8a2c3579 100644
--- a/packages/coding-agent/src/core/extensions/types.ts
+++ b/packages/coding-agent/src/core/extensions/types.ts
@@ -813,6 +813,9 @@ export interface ExtensionAPI {
 	/** Get the current session name, if set. */
 	getSessionName(): string | undefined;
 
+	/** Set or clear a label on an entry. Labels are user-defined markers for bookmarking/navigation. */
+	setLabel(entryId: string, label: string | undefined): void;
+
 	/** Execute a shell command. */
 	exec(command: string, args: string[], options?: ExecOptions): Promise<ExecResult>;
 
@@ -902,6 +905,8 @@ export type GetThinkingLevelHandler = () => ThinkingLevel;
 
 export type SetThinkingLevelHandler = (level: ThinkingLevel) => void;
 
+export type SetLabelHandler = (entryId: string, label: string | undefined) => void;
+
 /**
  * Shared state created by loader, used during registration and runtime.
  * Contains flag values (defaults set during registration, CLI values set after).
@@ -920,6 +925,7 @@ export interface ExtensionActions {
 	appendEntry: AppendEntryHandler;
 	setSessionName: SetSessionNameHandler;
 	getSessionName: GetSessionNameHandler;
+	setLabel: SetLabelHandler;
 	getActiveTools: GetActiveToolsHandler;
 	getAllTools: GetAllToolsHandler;
 	setActiveTools: SetActiveToolsHandler;
diff --git a/packages/coding-agent/src/modes/interactive/interactive-mode.ts b/packages/coding-agent/src/modes/interactive/interactive-mode.ts
index 534d03aa..1a267f4a 100644
--- a/packages/coding-agent/src/modes/interactive/interactive-mode.ts
+++ b/packages/coding-agent/src/modes/interactive/interactive-mode.ts
@@ -669,6 +669,9 @@ export class InteractiveMode {
 				getSessionName: () => {
 					return this.sessionManager.getSessionName();
 				},
+				setLabel: (entryId, label) => {
+					this.sessionManager.appendLabelChange(entryId, label);
+				},
 				getActiveTools: () => this.session.getActiveToolNames(),
 				getAllTools: () => this.session.getAllTools(),
 				setActiveTools: (toolNames) => this.session.setActiveToolsByName(toolNames),
diff --git a/packages/coding-agent/src/modes/print-mode.ts b/packages/coding-agent/src/modes/print-mode.ts
index 8af94fac..1a079718 100644
--- a/packages/coding-agent/src/modes/print-mode.ts
+++ b/packages/coding-agent/src/modes/print-mode.ts
@@ -60,6 +60,9 @@ export async function runPrintMode(session: AgentSession, options: PrintModeOpti
 				getSessionName: () => {
 					return session.sessionManager.getSessionName();
 				},
+				setLabel: (entryId, label) => {
+					session.sessionManager.appendLabelChange(entryId, label);
+				},
 				getActiveTools: () => session.getActiveToolNames(),
 				getAllTools: () => session.getAllTools(),
 				setActiveTools: (toolNames: string[]) => session.setActiveToolsByName(toolNames),
diff --git a/packages/coding-agent/src/modes/rpc/rpc-mode.ts b/packages/coding-agent/src/modes/rpc/rpc-mode.ts
index 11687b7b..95575bec 100644
--- a/packages/coding-agent/src/modes/rpc/rpc-mode.ts
+++ b/packages/coding-agent/src/modes/rpc/rpc-mode.ts
@@ -273,6 +273,9 @@ export async function runRpcMode(session: AgentSession): Promise<never> {
 				getSessionName: () => {
 					return session.sessionManager.getSessionName();
 				},
+				setLabel: (entryId, label) => {
+					session.sessionManager.appendLabelChange(entryId, label);
+				},
 				getActiveTools: () => session.getActiveToolNames(),
 				getAllTools: () => session.getAllTools(),
 				setActiveTools: (toolNames: string[]) => session.setActiveToolsByName(toolNames),
diff --git a/packages/coding-agent/test/compaction-extensions.test.ts b/packages/coding-agent/test/compaction-extensions.test.ts
index 62db5cce..4789e268 100644
--- a/packages/coding-agent/test/compaction-extensions.test.ts
+++ b/packages/coding-agent/test/compaction-extensions.test.ts
@@ -110,6 +110,7 @@ describe.skipIf(!API_KEY)("Compaction extensions", () => {
 				appendEntry: async () => {},
 				setSessionName: () => {},
 				getSessionName: () => undefined,
+				setLabel: () => {},
 				getActiveTools: () => [],
 				getAllTools: () => [],
 				setActiveTools: () => {},