diff --git a/Sources/DependencyCalculator/DependencyGraph.swift b/Sources/DependencyCalculator/DependencyGraph.swift
index c515078..cc36151 100644
--- a/Sources/DependencyCalculator/DependencyGraph.swift
+++ b/Sources/DependencyCalculator/DependencyGraph.swift
@@ -429,8 +429,7 @@ extension WorkspaceInfo {
     }
 
     /// Search all files specified in fileSystemSynchronizedGroups.
-    /// Currently, file extensions are note considered at all, so all files in the folder are subject to the search.
-    /// NOTE: FileSystemSynchronizedFileExceptionSet is not suppored yet.
+    /// Currently, file extensions are not considered at all, so all files in the folder are subject to the search.
     ///
     /// ref: https://github.com/tuist/XcodeGraph/pull/108
     /// The implementation of `XcodeGraph` only considers cases where the root is a folder.
@@ -450,8 +449,25 @@ extension WorkspaceInfo {
                 folderPath = group.path.map { Path($0) }
             }
             guard let folderPath else { return }
-            paths.append(contentsOf: (try? folderPath.recursiveChildren()) ?? [])
+
+            let membershipExceptionPaths = (group.exceptions ?? [])
+                .compactMap { $0 as? PBXFileSystemSynchronizedBuildFileExceptionSet }
+                .filter { $0.target.uuid == target.uuid }
+                .flatMap { $0.membershipExceptions ?? [] }
+                .map { folderPath + Path($0) }
+            let recursiveChildrenFilePaths = ((try? folderPath.recursiveChildren()) ?? [])
+                .filter { $0.isFile }
+
+            paths.append(contentsOf: recursiveChildrenFilePaths.filter { filePath in
+                !membershipExceptionPaths.contains { filePath.isDescendantOrSelf(of: $0) }
+            })
         }
         return paths
     }
 }
+
+private extension Path {
+    func isDescendantOrSelf(of path: Path) -> Bool {
+        self == path || string.hasPrefix(path.string + Path.separator)
+    }
+}
diff --git a/Tests/SelectiveTestingTests/ExampleProject/ExampleProject.xcodeproj/project.pbxproj b/Tests/SelectiveTestingTests/ExampleProject/ExampleProject.xcodeproj/project.pbxproj
index c3b31f5..6e7045f 100644
--- a/Tests/SelectiveTestingTests/ExampleProject/ExampleProject.xcodeproj/project.pbxproj
+++ b/Tests/SelectiveTestingTests/ExampleProject/ExampleProject.xcodeproj/project.pbxproj
@@ -94,8 +94,19 @@
 		B24BBDBF2CAD7244005E6DAC /* en */ = {isa = PBXFileReference; lastKnownFileType = text.plist.strings; name = en; path = en.lproj/Example.strings; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
+/* Begin PBXFileSystemSynchronizedBuildFileExceptionSet section */
+		095D76502FD30A2E007174DE /* PBXFileSystemSynchronizedBuildFileExceptionSet */ = {
+			isa = PBXFileSystemSynchronizedBuildFileExceptionSet;
+			membershipExceptions = (
+				Path/ExceptionView.swift,
+				Path/ExcludedFolder,
+			);
+			target = 276DB5BA29B144C900E5C615 /* ExampleProject */;
+		};
+/* End PBXFileSystemSynchronizedBuildFileExceptionSet section */
+
 /* Begin PBXFileSystemSynchronizedRootGroup section */
-		095EE0952DB8E35400EACE2E /* DeepFolder */ = {isa = PBXFileSystemSynchronizedRootGroup; explicitFileTypes = {}; explicitFolders = (); path = DeepFolder; sourceTree = "<group>"; };
+		095EE0952DB8E35400EACE2E /* DeepFolder */ = {isa = PBXFileSystemSynchronizedRootGroup; exceptions = (095D76502FD30A2E007174DE /* PBXFileSystemSynchronizedBuildFileExceptionSet */, ); explicitFileTypes = {}; explicitFolders = (Path/ExcludedFolder, ); path = DeepFolder; sourceTree = "<group>"; };
 /* End PBXFileSystemSynchronizedRootGroup section */
 
 /* Begin PBXFrameworksBuildPhase section */
diff --git a/Tests/SelectiveTestingTests/ExampleProject/ExampleProject/DeepFolder/Path/ExceptionView.swift b/Tests/SelectiveTestingTests/ExampleProject/ExampleProject/DeepFolder/Path/ExceptionView.swift
new file mode 100644
index 0000000..4f226ea
--- /dev/null
+++ b/Tests/SelectiveTestingTests/ExampleProject/ExampleProject/DeepFolder/Path/ExceptionView.swift
@@ -0,0 +1,7 @@
+import SwiftUI
+
+struct ExceptionView: View {
+    var body: some View {
+        EmptyView()
+    }
+}
diff --git a/Tests/SelectiveTestingTests/ExampleProject/ExampleProject/DeepFolder/Path/ExcludedFolder/ExcludedFolderView.swift b/Tests/SelectiveTestingTests/ExampleProject/ExampleProject/DeepFolder/Path/ExcludedFolder/ExcludedFolderView.swift
new file mode 100644
index 0000000..c283149
--- /dev/null
+++ b/Tests/SelectiveTestingTests/ExampleProject/ExampleProject/DeepFolder/Path/ExcludedFolder/ExcludedFolderView.swift
@@ -0,0 +1,7 @@
+import SwiftUI
+
+struct ExcludedFolderView: View {
+    var body: some View {
+        EmptyView()
+    }
+}
diff --git a/Tests/SelectiveTestingTests/SelectiveTestingProjectTests.swift b/Tests/SelectiveTestingTests/SelectiveTestingProjectTests.swift
index 1b5ea3a..d4d67d9 100644
--- a/Tests/SelectiveTestingTests/SelectiveTestingProjectTests.swift
+++ b/Tests/SelectiveTestingTests/SelectiveTestingProjectTests.swift
@@ -133,6 +133,42 @@ struct SelectiveTestingProjectTests {
         ]))
     }
 
+    @Test
+    func projectDeepFolderMembershipExceptionPathChange_turbo() async throws {
+        // given
+        let testTool = try IntegrationTestTool()
+        defer { try? testTool.tearDown() }
+
+        let tool = try testTool.createSUT(config: nil,
+                                          basePath: "ExampleProject.xcodeproj",
+                                          turbo: true)
+
+        // when
+        try testTool.changeFile(at: testTool.projectPath + "ExampleProject/DeepFolder/Path/ExceptionView.swift")
+
+        // then
+        let result = try await tool.run()
+        #expect(result == Set<TargetIdentity>())
+    }
+
+    @Test
+    func projectDeepFolderMembershipExceptionFolderChange_turbo() async throws {
+        // given
+        let testTool = try IntegrationTestTool()
+        defer { try? testTool.tearDown() }
+
+        let tool = try testTool.createSUT(config: nil,
+                                          basePath: "ExampleProject.xcodeproj",
+                                          turbo: true)
+
+        // when
+        try testTool.changeFile(at: testTool.projectPath + "ExampleProject/DeepFolder/Path/ExcludedFolder/ExcludedFolderView.swift")
+
+        // then
+        let result = try await tool.run()
+        #expect(result == Set<TargetIdentity>())
+    }
+
     @Test
     func projectTargetDependencyChange_turbo() async throws {
         // given
@@ -176,6 +212,40 @@ struct SelectiveTestingProjectTests {
         ]))
     }
 
+    @Test
+    func projectDeepFolderMembershipExceptionPathChange() async throws {
+        // given
+        let testTool = try IntegrationTestTool()
+        defer { try? testTool.tearDown() }
+
+        let tool = try testTool.createSUT(config: nil,
+                                          basePath: "ExampleProject.xcodeproj")
+
+        // when
+        try testTool.changeFile(at: testTool.projectPath + "ExampleProject/DeepFolder/Path/ExceptionView.swift")
+
+        // then
+        let result = try await tool.run()
+        #expect(result == Set<TargetIdentity>())
+    }
+
+    @Test
+    func projectDeepFolderMembershipExceptionFolderChange() async throws {
+        // given
+        let testTool = try IntegrationTestTool()
+        defer { try? testTool.tearDown() }
+
+        let tool = try testTool.createSUT(config: nil,
+                                          basePath: "ExampleProject.xcodeproj")
+
+        // when
+        try testTool.changeFile(at: testTool.projectPath + "ExampleProject/DeepFolder/Path/ExcludedFolder/ExcludedFolderView.swift")
+
+        // then
+        let result = try await tool.run()
+        #expect(result == Set<TargetIdentity>())
+    }
+
     @Test
     func projectLocalizedPathChange() async throws {
         // given