diff --git a/src/vs/workbench/contrib/chat/common/promptSyntax/hookSchema.ts b/src/vs/workbench/contrib/chat/common/promptSyntax/hookSchema.ts
index 8025b3ea67598..411f81483df3a 100644
--- a/src/vs/workbench/contrib/chat/common/promptSyntax/hookSchema.ts
+++ b/src/vs/workbench/contrib/chat/common/promptSyntax/hookSchema.ts
@@ -47,6 +47,55 @@ export type ChatRequestHooks = {
 	readonly [K in HookType]?: readonly IHookCommand[];
 };
 
+/**
+ * Computes a signature string for a hook command that captures all fields
+ * which determine whether two hooks would execute identically.
+ * Used for deduplication when the same hook is defined in multiple discovery paths.
+ * Uses JSON.stringify for unambiguous encoding (avoids collisions from
+ * separator characters in env keys/values).
+ */
+function computeHookSignature(hook: IHookCommand): string {
+	const envEntries = hook.env
+		? Object.entries(hook.env).sort(([a], [b]) => a.localeCompare(b))
+		: [];
+
+	return JSON.stringify({
+		command: hook.command ?? '',
+		windows: hook.windows ?? '',
+		linux: hook.linux ?? '',
+		osx: hook.osx ?? '',
+		cwd: hook.cwd?.toString() ?? '',
+		timeout: hook.timeout ?? null,
+		env: envEntries.length > 0 ? envEntries : null,
+	});
+}
+
+/**
+ * Removes duplicate hook commands from an array.
+ * Two hooks are considered identical if all their command fields (command, windows,
+ * linux, osx), cwd, env, and timeout match. This handles the case where the same
+ * hook is defined in multiple discovery paths (e.g., `.github/hooks/` and
+ * `.claude/settings.json`). First occurrence is kept, preserving path priority order.
+ */
+export function deduplicateHooks(hooks: readonly IHookCommand[]): readonly IHookCommand[] {
+	if (hooks.length <= 1) {
+		return hooks;
+	}
+
+	const seen = new Set<string>();
+	const result: IHookCommand[] = [];
+
+	for (const hook of hooks) {
+		const signature = computeHookSignature(hook);
+		if (!seen.has(signature)) {
+			seen.add(signature);
+			result.push(hook);
+		}
+	}
+
+	return result;
+}
+
 /**
  * Merges two sets of hooks by concatenating the command arrays for each hook type.
  * Additional hooks are appended after the base hooks.
diff --git a/src/vs/workbench/contrib/chat/common/promptSyntax/service/promptsServiceImpl.ts b/src/vs/workbench/contrib/chat/common/promptSyntax/service/promptsServiceImpl.ts
index 3a216261dedf5..c23e1484f597a 100644
--- a/src/vs/workbench/contrib/chat/common/promptSyntax/service/promptsServiceImpl.ts
+++ b/src/vs/workbench/contrib/chat/common/promptSyntax/service/promptsServiceImpl.ts
@@ -39,7 +39,7 @@ import { PromptFileParser, ParsedPromptFile, PromptHeaderAttributes } from '../p
 import { IAgentInstructions, type IAgentSource, IChatPromptSlashCommand, IConfiguredHooksInfo, ICustomAgent, IExtensionPromptPath, ILocalPromptPath, IPluginPromptPath, IPromptPath, IPromptsService, IAgentSkill, IUserPromptPath, PromptsStorage, ExtensionAgentSourceType, CUSTOM_AGENT_PROVIDER_ACTIVATION_EVENT, INSTRUCTIONS_PROVIDER_ACTIVATION_EVENT, IPromptFileContext, IPromptFileResource, PROMPT_FILE_PROVIDER_ACTIVATION_EVENT, SKILL_PROVIDER_ACTIVATION_EVENT, IPromptDiscoveryInfo, IPromptFileDiscoveryResult, IPromptSourceFolderResult, ICustomAgentVisibility, IResolvedAgentFile, AgentFileType, Logger, IPromptDiscoveryLogEntry } from './promptsService.js';
 import { Delayer } from '../../../../../../base/common/async.js';
 import { Schemas } from '../../../../../../base/common/network.js';
-import { ChatRequestHooks, IHookCommand, parseSubagentHooksFromYaml } from '../hookSchema.js';
+import { ChatRequestHooks, IHookCommand, deduplicateHooks, parseSubagentHooksFromYaml } from '../hookSchema.js';
 import { HookType } from '../hookTypes.js';
 import { HookSourceFormat, getHookSourceFormat, parseHooksFromFile } from '../hookCompatibility.js';
 import { IWorkspaceContextService } from '../../../../../../platform/workspace/common/workspace.js';
@@ -1367,6 +1367,16 @@ export class PromptsService extends Disposable implements IPromptsService {
 			return undefined;
 		}
 
+		// Deduplicate hooks that appear in multiple discovery paths
+		// (e.g., same hook in both .github/hooks/ and .claude/settings.json)
+		for (const [hookType, commands] of collectedHooks) {
+			const deduped = deduplicateHooks(commands);
+			if (deduped.length < commands.length) {
+				this.logger.trace(`[PromptsService] Deduplicated ${hookType} hooks: ${commands.length} → ${deduped.length}`);
+			}
+			collectedHooks.set(hookType, [...deduped]);
+		}
+
 		// Build the result
 		const result: ChatRequestHooks = Object.fromEntries(collectedHooks) as ChatRequestHooks;
 
diff --git a/src/vs/workbench/contrib/chat/test/common/promptSyntax/hookSchema.test.ts b/src/vs/workbench/contrib/chat/test/common/promptSyntax/hookSchema.test.ts
index ee30e3f60dc08..c85c15c48f092 100644
--- a/src/vs/workbench/contrib/chat/test/common/promptSyntax/hookSchema.test.ts
+++ b/src/vs/workbench/contrib/chat/test/common/promptSyntax/hookSchema.test.ts
@@ -5,7 +5,7 @@
 
 import assert from 'assert';
 import { ensureNoDisposablesAreLeakedInTestSuite } from '../../../../../../base/test/common/utils.js';
-import { resolveHookCommand, resolveEffectiveCommand, formatHookCommandLabel, IHookCommand, parseSubagentHooksFromYaml } from '../../../common/promptSyntax/hookSchema.js';
+import { resolveHookCommand, resolveEffectiveCommand, formatHookCommandLabel, IHookCommand, deduplicateHooks, parseSubagentHooksFromYaml } from '../../../common/promptSyntax/hookSchema.js';
 import { URI } from '../../../../../../base/common/uri.js';
 import { OperatingSystem } from '../../../../../../base/common/platform.js';
 import { HookType } from '../../../common/promptSyntax/hookTypes.js';
@@ -645,4 +645,119 @@ suite('HookSchema', () => {
 			assert.strictEqual(result[HookType.PreToolUse], undefined);
 		});
 	});
+
+	suite('deduplicateHooks', () => {
+		test('returns empty array unchanged', () => {
+			const result = deduplicateHooks([]);
+			assert.strictEqual(result.length, 0);
+		});
+
+		test('returns single hook unchanged', () => {
+			const hooks: IHookCommand[] = [{ type: 'command', command: 'echo test' }];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 1);
+			assert.deepStrictEqual(result[0], hooks[0]);
+		});
+
+		test('removes identical duplicate commands', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'echo hello' },
+				{ type: 'command', command: 'echo hello' },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 1);
+			assert.deepStrictEqual(result[0], hooks[0]);
+		});
+
+		test('preserves order of first occurrence', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'first' },
+				{ type: 'command', command: 'second' },
+				{ type: 'command', command: 'first' },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 2);
+			assert.strictEqual(result[0].command, 'first');
+			assert.strictEqual(result[1].command, 'second');
+		});
+
+		test('keeps hooks with different commands', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'echo a' },
+				{ type: 'command', command: 'echo b' },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 2);
+		});
+
+		test('keeps hooks with different cwd', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'npm test', cwd: URI.file('/workspace') },
+				{ type: 'command', command: 'npm test', cwd: URI.file('/workspace/src') },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 2);
+		});
+
+		test('keeps hooks with different timeout', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'validate', timeout: 30 },
+				{ type: 'command', command: 'validate', timeout: 60 },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 2);
+		});
+
+		test('keeps hooks with different env', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'npm test', env: { DEBUG: '1' } },
+				{ type: 'command', command: 'npm test' },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 2);
+		});
+
+		test('deduplicates hooks with identical env (order independent)', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'test', env: { A: '1', B: '2' } },
+				{ type: 'command', command: 'test', env: { B: '2', A: '1' } },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 1);
+		});
+
+		test('keeps hooks with different platform overrides', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'validate' },
+				{ type: 'command', command: 'validate', windows: 'validate.bat' },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 2);
+		});
+
+		test('deduplicates cross-path hooks with identical fields', () => {
+			// Simulates same hook defined in .github/hooks/ and .claude/settings.json
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'echo "AI disclosure reminder"', timeout: 5 },
+				{ type: 'command', command: 'echo "AI disclosure reminder"', timeout: 5 },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 1);
+		});
+
+		test('deduplicates multiple duplicates across many entries', () => {
+			const hooks: IHookCommand[] = [
+				{ type: 'command', command: 'hook-a' },
+				{ type: 'command', command: 'hook-b' },
+				{ type: 'command', command: 'hook-a' },
+				{ type: 'command', command: 'hook-c' },
+				{ type: 'command', command: 'hook-b' },
+			];
+			const result = deduplicateHooks(hooks);
+			assert.strictEqual(result.length, 3);
+			assert.strictEqual(result[0].command, 'hook-a');
+			assert.strictEqual(result[1].command, 'hook-b');
+			assert.strictEqual(result[2].command, 'hook-c');
+		});
+	});
 });