diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index 59827b2af..2ec3d9bd4 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -13,6 +13,7 @@
 
 ### Fixed
 
+- Fixed a redundant system prompt update (tools, rules) when an extension set the same active tools in a different order, for example a reversed `pi.setActiveTools()` list. Tools that stay active now keep their order and newly activated tools are appended ([#11495](https://github.com/earendil-works/pi/issues/11495))
 - Fixed `pi install` and `pi remove` adding ever deeper nested entries to the npm `package-lock.json` when the agent directory is reached through a symlink, such as `~/.pi` linked into a dotfiles repo. pi now passes the resolved real path to npm ([#11358](https://github.com/earendil-works/pi/issues/11358))
 - MCP sign-in now rejects authorization endpoints and other OAuth metadata URLs that are not `http:` or `https:`. Before, a malicious MCP server could supply a `file:` or custom protocol URL, which pi passed to the platform URL handler.
 - Automatic `fd` and `rg` downloads no longer fetch x86-64 binaries on ARM32 and other architectures without a prebuilt release. pi now warns and recommends installing the tool with the system package manager ([#11209](https://github.com/earendil-works/pi/issues/11209))
diff --git a/packages/coding-agent/src/core/agent-session.ts b/packages/coding-agent/src/core/agent-session.ts
index 3a9174cf6..c1529f019 100644
--- a/packages/coding-agent/src/core/agent-session.ts
+++ b/packages/coding-agent/src/core/agent-session.ts
@@ -1591,9 +1591,14 @@ export class AgentSession {
 	 * the registered, non-hidden ones; they are declared to the model. Active tools with a
 	 * `prepareLoadout` hook can change the declared descriptions and hide declarations from
 	 * requests (see {@link _installHiddenDeclarationsProjection}).
+	 *
+	 * The active tools are a set: tools that stay active keep their current order and newly active
+	 * ones are appended, so reordering the same names does not change the prompt (#11495).
 	 */
 	private _applyToolLoadout(toolNames: string[]): AgentTool[] {
-		const tools = [...new Set(toolNames)].flatMap((name) => {
+		const requested = new Set(toolNames);
+		const kept = this.getActiveToolNames().filter((name) => requested.has(name));
+		const tools = [...new Set([...kept, ...requested])].flatMap((name) => {
 			const tool = this._toolRegistry.get(name);
 			return tool && this._getToolExposure(name) !== "hidden" && this._isActivatable(name) ? [tool] : [];
 		});
diff --git a/packages/coding-agent/test/system-prompt-updates.test.ts b/packages/coding-agent/test/system-prompt-updates.test.ts
index a55c493d9..bbe5fb9f0 100644
--- a/packages/coding-agent/test/system-prompt-updates.test.ts
+++ b/packages/coding-agent/test/system-prompt-updates.test.ts
@@ -53,6 +53,23 @@ describe("system prompt updates", () => {
 		}
 	});
 
+	// #11495
+	test("does not patch the prompt when the active tools are only reordered", async () => {
+		const harness = await createHarness();
+		try {
+			harness.setResponses([fauxAssistantMessage("first"), fauxAssistantMessage("second")]);
+			await harness.session.prompt("one");
+			const before = harness.session.getActiveToolNames();
+			harness.session.setActiveToolsByName([...before].reverse());
+			expect(harness.session.getActiveToolNames()).toEqual(before);
+			await harness.session.prompt("two");
+			const systemMessages = harness.session.messages.filter((message) => message.role === "system");
+			expect(systemMessages).toHaveLength(1);
+		} finally {
+			harness.cleanup();
+		}
+	});
+
 	test("opens a transcript without a system message and declares the prompt on the first request", async () => {
 		const tempDir = mkdtempSync(join(tmpdir(), "pi-system-prompt-migration-"));
 		try {