diff --git a/packages/coding-agent/src/utils/git.ts b/packages/coding-agent/src/utils/git.ts
index d68e13868..ecd7c60de 100644
--- a/packages/coding-agent/src/utils/git.ts
+++ b/packages/coding-agent/src/utils/git.ts
@@ -561,10 +561,27 @@ function parsePackedRefs(content: string | null, targetRef: string): string | nu
 	return null;
 }
 
+function stripGitConfigComments(line: string): string {
+	let clean = "";
+	let inQuotes = false;
+	for (let i = 0; i < line.length; i++) {
+		const char = line[i];
+		if (char === '"') {
+			inQuotes = !inQuotes;
+			clean += char;
+		} else if (!inQuotes && (char === ";" || char === "#")) {
+			break;
+		} else {
+			clean += char;
+		}
+	}
+	return clean.trim();
+}
+
 function parseGitConfigHasReftable(content: string): boolean {
 	let inExtensions = false;
 	for (const line of content.split("\n")) {
-		const trimmed = line.trim();
+		const trimmed = stripGitConfigComments(line);
 		if (trimmed.startsWith("[") && trimmed.endsWith("]")) {
 			const section = trimmed.slice(1, -1).trim().toLowerCase();
 			inExtensions = section === "extensions";
@@ -572,27 +589,12 @@ function parseGitConfigHasReftable(content: string): boolean {
 			const eqIndex = trimmed.indexOf("=");
 			if (eqIndex !== -1) {
 				const key = trimmed.slice(0, eqIndex).trim().toLowerCase();
-				const value = trimmed.slice(eqIndex + 1).trim();
+				let value = trimmed.slice(eqIndex + 1).trim();
 				if (key === "refstorage") {
-					// Strip trailing comments per git-config(5)
-					let cleanValue = "";
-					let inQuotes = false;
-					for (let i = 0; i < value.length; i++) {
-						const char = value[i];
-						if (char === '"') {
-							inQuotes = !inQuotes;
-							cleanValue += char;
-						} else if (!inQuotes && (char === ";" || char === "#")) {
-							break;
-						} else {
-							cleanValue += char;
-						}
+					if (value.startsWith('"') && value.endsWith('"')) {
+						value = value.slice(1, -1).trim();
 					}
-					cleanValue = cleanValue.trim().toLowerCase();
-					if (cleanValue.startsWith('"') && cleanValue.endsWith('"')) {
-						cleanValue = cleanValue.slice(1, -1).trim();
-					}
-					if (cleanValue === "reftable") {
+					if (value.toLowerCase() === "reftable") {
 						return true;
 					}
 				}
diff --git a/packages/coding-agent/test/git-reftable.test.ts b/packages/coding-agent/test/git-reftable.test.ts
index df494edd1..1aa46f25c 100644
--- a/packages/coding-agent/test/git-reftable.test.ts
+++ b/packages/coding-agent/test/git-reftable.test.ts
@@ -158,6 +158,20 @@ describe.skipIf(!supportsReftable)("git reftable support", () => {
 			expect(await git.repo.isReftable(repository6)).toBe(true);
 			expect(git.repo.isReftableSync(repository6)).toBe(true);
 		}
+
+		// Test section header with trailing comment
+		const newConfigWithSectionComment = baseConfig.replace(
+			"[extensions]",
+			"[extensions] # extensions section comment",
+		);
+		await fs.writeFile(configPath, newConfigWithSectionComment);
+
+		const repository7 = await git.repo.resolve(testRepoDir);
+		expect(repository7).not.toBeNull();
+		if (repository7) {
+			expect(await git.repo.isReftable(repository7)).toBe(true);
+			expect(git.repo.isReftableSync(repository7)).toBe(true);
+		}
 	});
 
 	test("resolves references in a reftable worktree", async () => {