diff --git a/ChangeLog.md b/ChangeLog.md
index 72761bcad1..c82e0c8b76 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix analyzer [RCS1246](https://josefpihrt.github.io/docs/roslynator/analyzers/RCS1246) ([PR](https://github.com/dotnet/roslynator/pull/1460))
 - Fix analyzer [RCS1085](https://josefpihrt.github.io/docs/roslynator/analyzers/RCS1085) ([PR](https://github.com/dotnet/roslynator/pull/1461))
 - Fix analyzer [RCS1077](https://josefpihrt.github.io/docs/roslynator/analyzers/RCS1077) ([PR](https://github.com/dotnet/roslynator/pull/1463))
+- [CLI] Fix `roslynator analyze --include/--exclude` ([PR](https://github.com/dotnet/roslynator/pull/1459))
 
 ## [4.12.2] - 2024-04-23
 
diff --git a/src/Workspaces.Core/Diagnostics/CodeAnalyzer.cs b/src/Workspaces.Core/Diagnostics/CodeAnalyzer.cs
index 88f9c9b329..e1d0af929f 100644
--- a/src/Workspaces.Core/Diagnostics/CodeAnalyzer.cs
+++ b/src/Workspaces.Core/Diagnostics/CodeAnalyzer.cs
@@ -224,7 +224,13 @@ private IEnumerable<Diagnostic> FilterDiagnostics(IEnumerable<Diagnostic> diagno
                 else if (Options.ReportNotConfigurable
                     || !diagnostic.Descriptor.CustomTags.Contains(WellKnownDiagnosticTags.NotConfigurable))
                 {
-                    yield return diagnostic;
+                    SyntaxTree? tree = diagnostic.Location.SourceTree;
+
+                    if (tree is null
+                        || Options.FileSystemFilter?.IsMatch(tree.FilePath) != false)
+                    {
+                        yield return diagnostic;
+                    }
                 }
             }
         }