diff --git a/src/entrypoints/update-comment-link.ts b/src/entrypoints/update-comment-link.ts
index 849f954..f1be00e 100644
--- a/src/entrypoints/update-comment-link.ts
+++ b/src/entrypoints/update-comment-link.ts
@@ -15,6 +15,20 @@ import { GITHUB_SERVER_URL } from "../github/api/config";
 import { checkAndCommitOrDeleteBranch } from "../github/operations/branch-cleanup";
 import { updateClaudeComment } from "../github/operations/comments/update-claude-comment";
 
+/**
+ * Encodes a branch name for use in a URL, preserving forward slashes.
+ * GitHub expects literal slashes in branch names (e.g., /tree/feature/branch)
+ * but other special characters like parentheses need to be encoded.
+ * Note: encodeURIComponent doesn't encode ( ) ! ' * ~ per RFC 3986,
+ * but parentheses break markdown links so we encode them manually.
+ */
+function encodeBranchName(branchName: string): string {
+  return encodeURIComponent(branchName)
+    .replace(/%2F/gi, "/")
+    .replace(/\(/g, "%28")
+    .replace(/\)/g, "%29");
+}
+
 async function run() {
   try {
     const commentId = parseInt(process.env.CLAUDE_COMMENT_ID!);
@@ -140,7 +154,7 @@ async function run() {
             const prBody = encodeURIComponent(
               `This PR addresses ${entityType.toLowerCase()} #${context.entityNumber}\n\nGenerated with [Claude Code](https://claude.ai/code)`,
             );
-            const prUrl = `${serverUrl}/${owner}/${repo}/compare/${baseBranch}...${claudeBranch}?quick_pull=1&title=${prTitle}&body=${prBody}`;
+            const prUrl = `${serverUrl}/${owner}/${repo}/compare/${encodeBranchName(baseBranch)}...${encodeBranchName(claudeBranch)}?quick_pull=1&title=${prTitle}&body=${prBody}`;
             prLink = `\n[Create a PR](${prUrl})`;
           }
         } catch (error) {
diff --git a/src/github/operations/branch-cleanup.ts b/src/github/operations/branch-cleanup.ts
index 88de6de..d7f120c 100644
--- a/src/github/operations/branch-cleanup.ts
+++ b/src/github/operations/branch-cleanup.ts
@@ -2,6 +2,20 @@ import type { Octokits } from "../api/client";
 import { GITHUB_SERVER_URL } from "../api/config";
 import { $ } from "bun";
 
+/**
+ * Encodes a branch name for use in a URL, preserving forward slashes.
+ * GitHub expects literal slashes in branch names (e.g., /tree/feature/branch)
+ * but other special characters like parentheses need to be encoded.
+ * Note: encodeURIComponent doesn't encode ( ) ! ' * ~ per RFC 3986,
+ * but parentheses break markdown links so we encode them manually.
+ */
+function encodeBranchName(branchName: string): string {
+  return encodeURIComponent(branchName)
+    .replace(/%2F/gi, "/")
+    .replace(/\(/g, "%28")
+    .replace(/\)/g, "%29");
+}
+
 export async function checkAndCommitOrDeleteBranch(
   octokit: Octokits,
   owner: string,
@@ -80,7 +94,7 @@ export async function checkAndCommitOrDeleteBranch(
               );
 
               // Set branch link since we now have commits
-              const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
+              const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${encodeBranchName(claudeBranch)}`;
               branchLink = `\n[View branch](${branchUrl})`;
             } else {
               console.log(
@@ -91,7 +105,7 @@ export async function checkAndCommitOrDeleteBranch(
           } catch (gitError) {
             console.error("Error checking/committing changes:", gitError);
             // If we can't check git status, assume the branch might have changes
-            const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
+            const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${encodeBranchName(claudeBranch)}`;
             branchLink = `\n[View branch](${branchUrl})`;
           }
         } else {
@@ -102,13 +116,13 @@ export async function checkAndCommitOrDeleteBranch(
         }
       } else {
         // Only add branch link if there are commits
-        const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
+        const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${encodeBranchName(claudeBranch)}`;
         branchLink = `\n[View branch](${branchUrl})`;
       }
     } catch (error) {
       console.error("Error comparing commits on Claude branch:", error);
       // If we can't compare but the branch exists remotely, include the branch link
-      const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
+      const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${encodeBranchName(claudeBranch)}`;
       branchLink = `\n[View branch](${branchUrl})`;
     }
   }
diff --git a/src/github/operations/comment-logic.ts b/src/github/operations/comment-logic.ts
index 03b5d86..7032b20 100644
--- a/src/github/operations/comment-logic.ts
+++ b/src/github/operations/comment-logic.ts
@@ -1,5 +1,19 @@
 import { GITHUB_SERVER_URL } from "../api/config";
 
+/**
+ * Encodes a branch name for use in a URL, preserving forward slashes.
+ * GitHub expects literal slashes in branch names (e.g., /tree/feature/branch)
+ * but other special characters like parentheses need to be encoded.
+ * Note: encodeURIComponent doesn't encode ( ) ! ' * ~ per RFC 3986,
+ * but parentheses break markdown links so we encode them manually.
+ */
+function encodeBranchName(branchName: string): string {
+  return encodeURIComponent(branchName)
+    .replace(/%2F/gi, "/")
+    .replace(/\(/g, "%28")
+    .replace(/\)/g, "%29");
+}
+
 export type ExecutionDetails = {
   total_cost_usd?: number;
   duration_ms?: number;
@@ -160,7 +174,7 @@ export function updateCommentBody(input: CommentUpdateInput): string {
       // Extract owner/repo from jobUrl
       const repoMatch = jobUrl.match(/github\.com\/([^\/]+)\/([^\/]+)\//);
       if (repoMatch) {
-        branchUrl = `${GITHUB_SERVER_URL}/${repoMatch[1]}/${repoMatch[2]}/tree/${finalBranchName}`;
+        branchUrl = `${GITHUB_SERVER_URL}/${repoMatch[1]}/${repoMatch[2]}/tree/${encodeBranchName(finalBranchName)}`;
       }
     }
 
@@ -172,8 +186,9 @@ export function updateCommentBody(input: CommentUpdateInput): string {
   }
 
   // Add PR link (either from content or provided)
+  // Use greedy match with end anchor to capture full URL even if it contains parentheses
   const prUrl =
-    prLinkFromContent || (prLink ? prLink.match(/\(([^)]+)\)/)?.[1] : "");
+    prLinkFromContent || (prLink ? prLink.match(/\((.+)\)$/)?.[1] : "");
   if (prUrl) {
     links += ` • [Create PR ➔](${prUrl})`;
   }
diff --git a/src/github/operations/comments/common.ts b/src/github/operations/comments/common.ts
index df24c03..56b92d8 100644
--- a/src/github/operations/comments/common.ts
+++ b/src/github/operations/comments/common.ts
@@ -12,12 +12,26 @@ export function createJobRunLink(
   return `[View job run](${jobRunUrl})`;
 }
 
+/**
+ * Encodes a branch name for use in a URL, preserving forward slashes.
+ * GitHub expects literal slashes in branch names (e.g., /tree/feature/branch)
+ * but other special characters like parentheses need to be encoded.
+ * Note: encodeURIComponent doesn't encode ( ) ! ' * ~ per RFC 3986,
+ * but parentheses break markdown links so we encode them manually.
+ */
+function encodeBranchName(branchName: string): string {
+  return encodeURIComponent(branchName)
+    .replace(/%2F/gi, "/")
+    .replace(/\(/g, "%28")
+    .replace(/\)/g, "%29");
+}
+
 export function createBranchLink(
   owner: string,
   repo: string,
   branchName: string,
 ): string {
-  const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${branchName}`;
+  const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${encodeBranchName(branchName)}`;
   return `\n[View branch](${branchUrl})`;
 }
 
diff --git a/test/comment-logic.test.ts b/test/comment-logic.test.ts
index d55c82d..658eb8d 100644
--- a/test/comment-logic.test.ts
+++ b/test/comment-logic.test.ts
@@ -139,6 +139,21 @@ describe("updateCommentBody", () => {
       );
       expect(result).not.toContain("View branch");
     });
+
+    it("encodes special characters in branch names while preserving slashes", () => {
+      const input = {
+        ...baseInput,
+        branchName: "feature/fix(issue)-test",
+      };
+
+      const result = updateCommentBody(input);
+      // Branch name display should show the original name
+      expect(result).toContain("`feature/fix(issue)-test`");
+      // URL should have encoded parentheses but preserved slashes
+      expect(result).toContain(
+        "https://github.com/owner/repo/tree/feature/fix%28issue%29-test",
+      );
+    });
   });
 
   describe("PR link", () => {