diff --git a/.changeset/init-gitignore-dedupe.md b/.changeset/init-gitignore-dedupe.md
new file mode 100644
index 000000000..90350db88
--- /dev/null
+++ b/.changeset/init-gitignore-dedupe.md
@@ -0,0 +1,5 @@
+---
+"clerk": patch
+---
+
+Stop adding a duplicate `.clerk/` line to `.gitignore` when the folder is already ignored under an equivalent pattern such as `/.clerk/`, `.clerk`, or `.clerk/*`.
diff --git a/packages/cli-core/src/commands/init/README.md b/packages/cli-core/src/commands/init/README.md
index 666adbc69..420b8d2ca 100644
--- a/packages/cli-core/src/commands/init/README.md
+++ b/packages/cli-core/src/commands/init/README.md
@@ -346,7 +346,7 @@ In accountless mode, after calling `POST /v1/accountless_applications`, `clerk i
 }
 ```
 
-`.clerk/` is automatically added to `.gitignore` when the breadcrumb is written. The breadcrumb is removed after a successful claim (or when the claim token expires/is already consumed).
+When `clerk init` writes the breadcrumb, it adds `.clerk/` to `.gitignore` unless an equivalent pattern such as `/.clerk/`, `.clerk`, or `.clerk/*` already ignores the folder. The next `clerk auth login` tries to claim the application and removes the breadcrumb if the claim succeeds or the token has expired. See the [breadcrumb lifecycle](../auth/README.md#accountless-autoclaim-breadcrumb-lifecycle) for every case.
 
 ### Re-running init on an already-accountless project
 
diff --git a/packages/cli-core/src/lib/git.test.ts b/packages/cli-core/src/lib/git.test.ts
index eea94dfea..5a7fe698a 100644
--- a/packages/cli-core/src/lib/git.test.ts
+++ b/packages/cli-core/src/lib/git.test.ts
@@ -1,5 +1,8 @@
-import { test, expect, describe } from "bun:test";
-import { normalizeGitRemoteUrl } from "./git.ts";
+import { test, expect, describe, beforeEach, afterEach } from "bun:test";
+import { mkdtemp, rm } from "node:fs/promises";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+import { ensureGitignoreEntry, normalizeGitRemoteUrl } from "./git.ts";
 
 describe("normalizeGitRemoteUrl", () => {
   test("normalizes SSH SCP-style URL", () => {
@@ -66,3 +69,94 @@ describe("normalizeGitRemoteUrl", () => {
     );
   });
 });
+
+describe("ensureGitignoreEntry", () => {
+  let tempDir: string;
+  let gitignorePath: string;
+
+  beforeEach(async () => {
+    tempDir = await mkdtemp(join(tmpdir(), "clerk-git-test-"));
+    gitignorePath = join(tempDir, ".gitignore");
+  });
+
+  afterEach(async () => {
+    await rm(tempDir, { recursive: true, force: true });
+  });
+
+  test("creates .gitignore when none exists", async () => {
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe(".clerk/\n");
+  });
+
+  test("appends the entry when it is not listed", async () => {
+    await Bun.write(gitignorePath, "node_modules\n");
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe("node_modules\n.clerk/\n");
+  });
+
+  test("adds a newline before appending when the file lacks a trailing one", async () => {
+    await Bun.write(gitignorePath, "node_modules");
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe("node_modules\n.clerk/\n");
+  });
+
+  test.each([
+    ".clerk/",
+    "/.clerk/",
+    "/.clerk",
+    ".clerk",
+    ".clerk/*",
+    ".clerk/**",
+    "/.clerk/  ",
+    "/.clerk/\r",
+    "/.clerk/ \r",
+  ])("leaves .gitignore unchanged when %p is already listed", async (existing) => {
+    const content = `node_modules\n# clerk configuration (can include secrets)\n${existing}\n`;
+    await Bun.write(gitignorePath, content);
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe(content);
+  });
+
+  test("does not treat a commented-out entry as listed", async () => {
+    await Bun.write(gitignorePath, "# .clerk/\n");
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe("# .clerk/\n.clerk/\n");
+  });
+
+  test("does not treat a negated entry as listed", async () => {
+    await Bun.write(gitignorePath, "!.clerk/\n");
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe("!.clerk/\n.clerk/\n");
+  });
+
+  test("does not treat an entry with leading whitespace as listed", async () => {
+    await Bun.write(gitignorePath, "  /.clerk/\n");
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe("  /.clerk/\n.clerk/\n");
+  });
+
+  test("does not treat an entry with a trailing tab as listed", async () => {
+    await Bun.write(gitignorePath, "/.clerk/\t\n");
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe("/.clerk/\t\n.clerk/\n");
+  });
+
+  test("appends the entry when a later negation re-includes the folder", async () => {
+    await Bun.write(gitignorePath, "/.clerk/\n!.clerk/\n");
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe("/.clerk/\n!.clerk/\n.clerk/\n");
+  });
+
+  test("leaves .gitignore unchanged when the entry follows a negation", async () => {
+    const content = "!.clerk/\n/.clerk/\n";
+    await Bun.write(gitignorePath, content);
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe(content);
+  });
+
+  test("does not treat a nested path as listed", async () => {
+    await Bun.write(gitignorePath, "apps/web/.clerk/\n");
+    await ensureGitignoreEntry(tempDir, ".clerk/");
+    expect(await Bun.file(gitignorePath).text()).toBe("apps/web/.clerk/\n.clerk/\n");
+  });
+});
diff --git a/packages/cli-core/src/lib/git.ts b/packages/cli-core/src/lib/git.ts
index 34fced039..d39398e24 100644
--- a/packages/cli-core/src/lib/git.ts
+++ b/packages/cli-core/src/lib/git.ts
@@ -102,7 +102,17 @@ export function normalizeGitRemoteUrl(raw: string): string {
 }
 
 /**
- * Adds `entry` to the project's `.gitignore` unless it is already listed.
+ * Reduces a root-level ignore pattern to its bare path so equivalent spellings
+ * compare equal: `/.clerk/`, `.clerk/`, `/.clerk`, `.clerk`, and `.clerk/*`
+ * all become `.clerk`.
+ */
+function normalizeGitignorePattern(pattern: string): string {
+  return pattern.replace(/^\//, "").replace(/\/\*{0,2}$/, "");
+}
+
+/**
+ * Adds `entry` to the project's `.gitignore` unless it, or an equivalent
+ * pattern such as `/.clerk/` for `.clerk/`, is already listed.
  *
  * The CLI writes files into a user's repository that must not be committed,
  * such as the keyless breadcrumb. Creating one without this is how a live
@@ -113,8 +123,18 @@ export async function ensureGitignoreEntry(cwd: string, entry: string): Promise<
   const content = await Bun.file(gitignorePath)
     .text()
     .catch(() => "");
-  const lines = content.split("\n").map((l) => l.trim());
-  if (lines.includes(entry)) return;
+  const target = normalizeGitignorePattern(entry);
+  // Git strips a trailing CR and trailing spaces, but keeps tabs and leading
+  // whitespace. The last matching rule wins, so a later `!.clerk/` re-includes
+  // the folder.
+  let listed = false;
+  for (const line of content.split("\n").map((l) => l.replace(/\r$/, "").replace(/ +$/, ""))) {
+    if (!line || line.startsWith("#")) continue;
+    const negated = line.startsWith("!");
+    const pattern = negated ? line.slice(1) : line;
+    if (normalizeGitignorePattern(pattern) === target) listed = !negated;
+  }
+  if (listed) return;
   const separator = content && !content.endsWith("\n") ? "\n" : "";
   await Bun.write(gitignorePath, `${content}${separator}${entry}\n`);
   log.debug(`git: added ${entry} to .gitignore`);