diff --git a/README.md b/README.md
index 6da46c00e..64b68a37a 100644
--- a/README.md
+++ b/README.md
@@ -752,6 +752,7 @@ The following sets of tools are available:
 - **assign_copilot_to_issue** - Assign Copilot to issue
   - **Required OAuth Scopes**: `repo`
   - `base_ref`: Git reference (e.g., branch) that the agent will start its work from. If not specified, defaults to the repository's default branch (string, optional)
+  - `custom_instructions`: Optional custom instructions to guide the agent beyond the issue body. Use this to provide additional context, constraints, or guidance that is not captured in the issue description (string, optional)
   - `issue_number`: Issue number (number, required)
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
diff --git a/pkg/github/__toolsnaps__/assign_copilot_to_issue.snap b/pkg/github/__toolsnaps__/assign_copilot_to_issue.snap
index 7ad1922a0..81ea90e5a 100644
--- a/pkg/github/__toolsnaps__/assign_copilot_to_issue.snap
+++ b/pkg/github/__toolsnaps__/assign_copilot_to_issue.snap
@@ -11,6 +11,10 @@
         "type": "string",
         "description": "Git reference (e.g., branch) that the agent will start its work from. If not specified, defaults to the repository's default branch"
       },
+      "custom_instructions": {
+        "type": "string",
+        "description": "Optional custom instructions to guide the agent beyond the issue body. Use this to provide additional context, constraints, or guidance that is not captured in the issue description"
+      },
       "issue_number": {
         "type": "number",
         "description": "Issue number"
diff --git a/pkg/github/issues.go b/pkg/github/issues.go
index 63174c9e9..3d57165d5 100644
--- a/pkg/github/issues.go
+++ b/pkg/github/issues.go
@@ -1650,6 +1650,10 @@ func AssignCopilotToIssue(t translations.TranslationHelperFunc) inventory.Server
 						Type:        "string",
 						Description: "Git reference (e.g., branch) that the agent will start its work from. If not specified, defaults to the repository's default branch",
 					},
+					"custom_instructions": {
+						Type:        "string",
+						Description: "Optional custom instructions to guide the agent beyond the issue body. Use this to provide additional context, constraints, or guidance that is not captured in the issue description",
+					},
 				},
 				Required: []string{"owner", "repo", "issue_number"},
 			},
@@ -1657,10 +1661,11 @@ func AssignCopilotToIssue(t translations.TranslationHelperFunc) inventory.Server
 		[]scopes.Scope{scopes.Repo},
 		func(ctx context.Context, deps ToolDependencies, _ *mcp.CallToolRequest, args map[string]any) (*mcp.CallToolResult, any, error) {
 			var params struct {
-				Owner       string `mapstructure:"owner"`
-				Repo        string `mapstructure:"repo"`
-				IssueNumber int32  `mapstructure:"issue_number"`
-				BaseRef     string `mapstructure:"base_ref"`
+				Owner              string `mapstructure:"owner"`
+				Repo               string `mapstructure:"repo"`
+				IssueNumber        int32  `mapstructure:"issue_number"`
+				BaseRef            string `mapstructure:"base_ref"`
+				CustomInstructions string `mapstructure:"custom_instructions"`
 			}
 			if err := mapstructure.Decode(args, &params); err != nil {
 				return utils.NewToolResultError(err.Error()), nil, nil
@@ -1775,6 +1780,12 @@ func AssignCopilotToIssue(t translations.TranslationHelperFunc) inventory.Server
 				agentAssignment.BaseRef = &baseRef
 			}
 
+			// Add custom instructions if provided
+			if params.CustomInstructions != "" {
+				customInstructions := githubv4.String(params.CustomInstructions)
+				agentAssignment.CustomInstructions = &customInstructions
+			}
+
 			// Execute the updateIssue mutation with the GraphQL-Features header
 			// This header is required for the agent assignment API which is not GA yet
 			var updateIssueMutation struct {
diff --git a/pkg/github/issues_test.go b/pkg/github/issues_test.go
index 21e78874a..0d9070ace 100644
--- a/pkg/github/issues_test.go
+++ b/pkg/github/issues_test.go
@@ -2086,6 +2086,7 @@ func TestAssignCopilotToIssue(t *testing.T) {
 	assert.Contains(t, tool.InputSchema.(*jsonschema.Schema).Properties, "repo")
 	assert.Contains(t, tool.InputSchema.(*jsonschema.Schema).Properties, "issue_number")
 	assert.Contains(t, tool.InputSchema.(*jsonschema.Schema).Properties, "base_ref")
+	assert.Contains(t, tool.InputSchema.(*jsonschema.Schema).Properties, "custom_instructions")
 	assert.ElementsMatch(t, tool.InputSchema.(*jsonschema.Schema).Required, []string{"owner", "repo", "issue_number"})
 
 	// Helper function to create pointer to githubv4.String
@@ -2638,6 +2639,116 @@ func TestAssignCopilotToIssue(t *testing.T) {
 				),
 			),
 		},
+		{
+			name: "successful assignment with custom_instructions specified",
+			requestArgs: map[string]any{
+				"owner":               "owner",
+				"repo":                "repo",
+				"issue_number":        float64(123),
+				"custom_instructions": "Please ensure all code follows PEP 8 style guidelines and includes comprehensive docstrings",
+			},
+			mockedClient: githubv4mock.NewMockedHTTPClient(
+				githubv4mock.NewQueryMatcher(
+					struct {
+						Repository struct {
+							SuggestedActors struct {
+								Nodes []struct {
+									Bot struct {
+										ID       githubv4.ID
+										Login    githubv4.String
+										TypeName string `graphql:"__typename"`
+									} `graphql:"... on Bot"`
+								}
+								PageInfo struct {
+									HasNextPage bool
+									EndCursor   string
+								}
+							} `graphql:"suggestedActors(first: 100, after: $endCursor, capabilities: CAN_BE_ASSIGNED)"`
+						} `graphql:"repository(owner: $owner, name: $name)"`
+					}{},
+					map[string]any{
+						"owner":     githubv4.String("owner"),
+						"name":      githubv4.String("repo"),
+						"endCursor": (*githubv4.String)(nil),
+					},
+					githubv4mock.DataResponse(map[string]any{
+						"repository": map[string]any{
+							"suggestedActors": map[string]any{
+								"nodes": []any{
+									map[string]any{
+										"id":         githubv4.ID("copilot-swe-agent-id"),
+										"login":      githubv4.String("copilot-swe-agent"),
+										"__typename": "Bot",
+									},
+								},
+							},
+						},
+					}),
+				),
+				githubv4mock.NewQueryMatcher(
+					struct {
+						Repository struct {
+							ID    githubv4.ID
+							Issue struct {
+								ID        githubv4.ID
+								Assignees struct {
+									Nodes []struct {
+										ID githubv4.ID
+									}
+								} `graphql:"assignees(first: 100)"`
+							} `graphql:"issue(number: $number)"`
+						} `graphql:"repository(owner: $owner, name: $name)"`
+					}{},
+					map[string]any{
+						"owner":  githubv4.String("owner"),
+						"name":   githubv4.String("repo"),
+						"number": githubv4.Int(123),
+					},
+					githubv4mock.DataResponse(map[string]any{
+						"repository": map[string]any{
+							"id": githubv4.ID("test-repo-id"),
+							"issue": map[string]any{
+								"id": githubv4.ID("test-issue-id"),
+								"assignees": map[string]any{
+									"nodes": []any{},
+								},
+							},
+						},
+					}),
+				),
+				githubv4mock.NewMutationMatcher(
+					struct {
+						UpdateIssue struct {
+							Issue struct {
+								ID     githubv4.ID
+								Number githubv4.Int
+								URL    githubv4.String
+							}
+						} `graphql:"updateIssue(input: $input)"`
+					}{},
+					UpdateIssueInput{
+						ID:          githubv4.ID("test-issue-id"),
+						AssigneeIDs: []githubv4.ID{githubv4.ID("copilot-swe-agent-id")},
+						AgentAssignment: &AgentAssignmentInput{
+							BaseRef:            nil,
+							CustomAgent:        ptrGitHubv4String(""),
+							CustomInstructions: ptrGitHubv4String("Please ensure all code follows PEP 8 style guidelines and includes comprehensive docstrings"),
+							TargetRepositoryID: githubv4.ID("test-repo-id"),
+						},
+					},
+					nil,
+					githubv4mock.DataResponse(map[string]any{
+						"updateIssue": map[string]any{
+							"issue": map[string]any{
+								"id":     githubv4.ID("test-issue-id"),
+								"number": githubv4.Int(123),
+								"url":    githubv4.String("https://github.com/owner/repo/issues/123"),
+							},
+						},
+					}),
+				),
+			),
+		},
 	}
 
 	for _, tc := range tests {