diff --git a/actions/setup/js/assign_agent_helpers.cjs b/actions/setup/js/assign_agent_helpers.cjs
index af5676d9840..dcf2c838275 100644
--- a/actions/setup/js/assign_agent_helpers.cjs
+++ b/actions/setup/js/assign_agent_helpers.cjs
@@ -403,6 +403,13 @@ async function assignAgentToIssue(
       issue_number: issueNumber,
       assignees: [assignee],
     };
+    const agentAssignment = {};
+    if (pullRequestRepoSlug != null) agentAssignment.target_repo = pullRequestRepoSlug;
+    if (baseBranch != null) agentAssignment.base_branch = baseBranch;
+    if (customInstructions != null) agentAssignment.custom_instructions = customInstructions;
+    if (customAgent != null) agentAssignment.custom_agent = customAgent;
+    if (model != null) agentAssignment.model = model;
+    if (Object.keys(agentAssignment).length > 0) assignParams.agent_assignment = agentAssignment;
     await githubClient.request("POST /repos/{owner}/{repo}/issues/{issue_number}/assignees", assignParams);
     return true;
   } catch (error) {
diff --git a/actions/setup/js/assign_agent_helpers.test.cjs b/actions/setup/js/assign_agent_helpers.test.cjs
index f161106b9e5..84c5784092f 100644
--- a/actions/setup/js/assign_agent_helpers.test.cjs
+++ b/actions/setup/js/assign_agent_helpers.test.cjs
@@ -456,6 +456,96 @@ describe("assign_agent_helpers.cjs", () => {
       expect(mockCore.error).toHaveBeenCalledWith(expect.stringContaining("GH_AW_AGENT_TOKEN"));
       expect(mockCore.info).toHaveBeenCalledWith(expect.stringContaining("github.github.com/gh-aw/reference/copilot-cloud-agent/#authentication"));
     });
+
+    it("should not include agent_assignment when all optional fields are null", async () => {
+      const mockRequest = vi.fn().mockResolvedValue({ status: 201 });
+      const restClient = { request: mockRequest };
+
+      await assignAgentToIssue("id", "copilot-swe-agent[bot]", [], "copilot", null, null, null, null, null, restClient, taskContext);
+
+      expect(mockRequest).toHaveBeenCalledWith("POST /repos/{owner}/{repo}/issues/{issue_number}/assignees", {
+        owner: "myorg",
+        repo: "myrepo",
+        issue_number: 42,
+        assignees: ["copilot-swe-agent[bot]"],
+      });
+    });
+
+    it("should include agent_assignment with all fields when all are provided", async () => {
+      const mockRequest = vi.fn().mockResolvedValue({ status: 201 });
+      const restClient = { request: mockRequest };
+
+      await assignAgentToIssue("id", "copilot-swe-agent[bot]", [], "copilot", null, "claude-opus-4.6", "my-agent", "Follow the coding guidelines.", "feature-branch", restClient, taskContext, "otherorg/otherrepo");
+
+      expect(mockRequest).toHaveBeenCalledWith("POST /repos/{owner}/{repo}/issues/{issue_number}/assignees", {
+        owner: "myorg",
+        repo: "myrepo",
+        issue_number: 42,
+        assignees: ["copilot-swe-agent[bot]"],
+        agent_assignment: {
+          target_repo: "otherorg/otherrepo",
+          base_branch: "feature-branch",
+          custom_instructions: "Follow the coding guidelines.",
+          custom_agent: "my-agent",
+          model: "claude-opus-4.6",
+        },
+      });
+    });
+
+    it("should include agent_assignment with only the provided fields", async () => {
+      const mockRequest = vi.fn().mockResolvedValue({ status: 201 });
+      const restClient = { request: mockRequest };
+
+      await assignAgentToIssue("id", "copilot-swe-agent[bot]", [], "copilot", null, null, null, "Always write tests.", null, restClient, taskContext);
+
+      expect(mockRequest).toHaveBeenCalledWith("POST /repos/{owner}/{repo}/issues/{issue_number}/assignees", {
+        owner: "myorg",
+        repo: "myrepo",
+        issue_number: 42,
+        assignees: ["copilot-swe-agent[bot]"],
+        agent_assignment: {
+          custom_instructions: "Always write tests.",
+        },
+      });
+    });
+
+    it("should include agent_assignment with target_repo when pullRequestRepoSlug is provided", async () => {
+      const mockRequest = vi.fn().mockResolvedValue({ status: 201 });
+      const restClient = { request: mockRequest };
+
+      await assignAgentToIssue("id", "copilot-swe-agent[bot]", [], "copilot", null, null, null, null, null, restClient, taskContext, "otherorg/otherrepo");
+
+      expect(mockRequest).toHaveBeenCalledWith("POST /repos/{owner}/{repo}/issues/{issue_number}/assignees", {
+        owner: "myorg",
+        repo: "myrepo",
+        issue_number: 42,
+        assignees: ["copilot-swe-agent[bot]"],
+        agent_assignment: {
+          target_repo: "otherorg/otherrepo",
+        },
+      });
+    });
+
+    it("should include empty-string agent_assignment fields when explicitly provided", async () => {
+      const mockRequest = vi.fn().mockResolvedValue({ status: 201 });
+      const restClient = { request: mockRequest };
+
+      await assignAgentToIssue("id", "copilot-swe-agent[bot]", [], "copilot", null, "", "", "", "", restClient, taskContext, "");
+
+      expect(mockRequest).toHaveBeenCalledWith("POST /repos/{owner}/{repo}/issues/{issue_number}/assignees", {
+        owner: "myorg",
+        repo: "myrepo",
+        issue_number: 42,
+        assignees: ["copilot-swe-agent[bot]"],
+        agent_assignment: {
+          target_repo: "",
+          base_branch: "",
+          custom_instructions: "",
+          custom_agent: "",
+          model: "",
+        },
+      });
+    });
   });
 
   describe("generatePermissionErrorSummary", () => {
diff --git a/actions/setup/js/assign_to_agent.cjs b/actions/setup/js/assign_to_agent.cjs
index 064a7fab4e2..21868685ce5 100644
--- a/actions/setup/js/assign_to_agent.cjs
+++ b/actions/setup/js/assign_to_agent.cjs
@@ -244,6 +244,7 @@ async function main(config = {}) {
 
     // Handle per-item pull_request_repo override
     let effectivePullRequestRepoSlug = basePullRequestRepoSlug;
+    let effectivePullRequestBaseBranch = effectiveBaseBranch;
     let hasValidatedPerItemPullRequestRepoOverride = false;
     const hasPullRequestRepoOverrideField = message.pull_request_repo != null;
     const trimmedPullRequestRepoOverride = typeof message.pull_request_repo === "string" ? message.pull_request_repo.trim() : "";
@@ -260,8 +261,9 @@ async function main(config = {}) {
           return { success: false, error };
         }
         try {
-          await resolvePullRequestRepo(githubClient, pullRequestRepoParts[0], pullRequestRepoParts[1], configuredBaseBranch);
+          const resolvedPullRequestRepo = await resolvePullRequestRepo(githubClient, pullRequestRepoParts[0], pullRequestRepoParts[1], configuredBaseBranch);
           effectivePullRequestRepoSlug = itemPullRequestRepo;
+          effectivePullRequestBaseBranch = resolvedPullRequestRepo.effectiveBaseBranch;
           hasValidatedPerItemPullRequestRepoOverride = true;
           core.info(`Using per-item pull request repository: ${itemPullRequestRepo}`);
         } catch (error) {
@@ -389,7 +391,7 @@ async function main(config = {}) {
       if (model) core.info(`Using model: ${model}`);
       if (customAgent) core.info(`Using custom agent: ${customAgent}`);
       if (customInstructions) core.info(`Using custom instructions: ${customInstructions.substring(0, 100)}${customInstructions.length > 100 ? "..." : ""}`);
-      if (effectiveBaseBranch) core.info(`Using base branch: ${effectiveBaseBranch}`);
+      if (effectivePullRequestBaseBranch) core.info(`Using base branch: ${effectivePullRequestBaseBranch}`);
 
       const success = await assignAgentToIssue(
         assignableId,
@@ -400,7 +402,7 @@ async function main(config = {}) {
         model,
         customAgent,
         customInstructions,
-        effectiveBaseBranch,
+        effectivePullRequestBaseBranch,
         githubClient,
         taskContext,
         effectivePullRequestRepoSlug,
diff --git a/actions/setup/js/assign_to_agent.test.cjs b/actions/setup/js/assign_to_agent.test.cjs
index fd9832bcff6..d2b4731824a 100644
--- a/actions/setup/js/assign_to_agent.test.cjs
+++ b/actions/setup/js/assign_to_agent.test.cjs
@@ -1496,7 +1496,7 @@ describe("assign_to_agent", () => {
     // Get global PR repository ID and default branch (for default-pr-repo)
     mockGithub.rest.repos.get.mockResolvedValueOnce({ data: { node_id: "default-pr-repo-id", default_branch: "main" } });
     // Get item PR repository
-    mockGithub.rest.repos.get.mockResolvedValueOnce({ data: { node_id: "item-pull-request-repo-id", default_branch: "main" } });
+    mockGithub.rest.repos.get.mockResolvedValueOnce({ data: { node_id: "item-pull-request-repo-id", default_branch: "develop" } });
     // Find agent
     mockGithub.rest.issues.checkUserCanBeAssigned.mockResolvedValueOnce({});
     mockGithub.rest.users.getByUsername.mockResolvedValueOnce({ data: { id: 99999 } });
@@ -1511,7 +1511,16 @@ describe("assign_to_agent", () => {
 
     expect(mockCore.info).toHaveBeenCalledWith(expect.stringContaining("Using per-item pull request repository: test-owner/item-pull-request-repo"));
 
-    expect(mockGithub.request).toHaveBeenCalledWith("POST /repos/{owner}/{repo}/issues/{issue_number}/assignees", expect.objectContaining({ owner: "test-owner", repo: "test-repo", issue_number: 42 }));
+    expect(mockGithub.request).toHaveBeenLastCalledWith("POST /repos/{owner}/{repo}/issues/{issue_number}/assignees", {
+      owner: "test-owner",
+      repo: "test-repo",
+      issue_number: 42,
+      assignees: ["copilot-swe-agent[bot]"],
+      agent_assignment: {
+        target_repo: "test-owner/item-pull-request-repo",
+        base_branch: "develop",
+      },
+    });
   });
 
   it("should reject per-item pull_request_repo not in allowed list", async () => {