diff --git a/ChangeLog.md b/ChangeLog.md
index cd73a99478..ae18faed37 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix enum contained flags check for partial matches in [RCS1258](https://josefpihrt.github.io/docs/roslynator/analyzers/RCS1258) ([PR](https://github.com/dotnet/roslynator/pull/1740) by @ovska)
 - Fix analyzer [RCS1146](https://josefpihrt.github.io/docs/roslynator/analyzers/RCS1146) ([PR](https://github.com/dotnet/roslynator/pull/1747))
 - Fix analyzer [RCS1194](https://josefpihrt.github.io/docs/roslynator/analyzers/RCS1194) ([PR](https://github.com/dotnet/roslynator/pull/1733))
+- [CLI] Fix `fix` command ignoring `--include` / `--exclude` file filter ([PR](https://github.com/dotnet/roslynator/pull/1758) by @hashiiiii)
 
 ## [4.15.0] - 2025-12-14
 
diff --git a/src/Workspaces.Core/CodeFixes/CodeFixer.cs b/src/Workspaces.Core/CodeFixes/CodeFixer.cs
index 4d58974c86..fdc7e2d31a 100644
--- a/src/Workspaces.Core/CodeFixes/CodeFixer.cs
+++ b/src/Workspaces.Core/CodeFixes/CodeFixer.cs
@@ -294,12 +294,16 @@ ImmutableArray<Diagnostic> GetFixableDiagnostics(
             IEnumerable<Diagnostic> fixableCompilerDiagnostics = compilerDiagnostics
                 .Where(f => f.Severity != DiagnosticSeverity.Error
                     && !Options.IgnoredCompilerDiagnosticIds.Contains(f.Id)
-                    && fixersById.ContainsKey(f.Id));
+                    && fixersById.ContainsKey(f.Id)
+                    && (f.Location.SourceTree is null
+                        || Options.FileSystemFilter?.IsMatch(f.Location.SourceTree.FilePath) != false));
 
             return diagnostics
                 .Where(f => f.IsEffective(Options, project.CompilationOptions)
                     && analyzersById.ContainsKey(f.Id)
-                    && fixersById.ContainsKey(f.Id))
+                    && fixersById.ContainsKey(f.Id)
+                    && (f.Location.SourceTree is null
+                        || Options.FileSystemFilter?.IsMatch(f.Location.SourceTree.FilePath) != false))
                 .Concat(fixableCompilerDiagnostics)
                 .ToImmutableArray();
         }
@@ -357,7 +361,10 @@ private async Task<DiagnosticFixResult> FixDiagnosticsAsync(
             }
 
             diagnostics = diagnostics
-                .Where(f => f.Id == descriptor.Id && f.Severity >= Options.SeverityLevel)
+                .Where(f => f.Id == descriptor.Id
+                    && f.Severity >= Options.SeverityLevel
+                    && (f.Location.SourceTree is null
+                        || Options.FileSystemFilter?.IsMatch(f.Location.SourceTree.FilePath) != false))
                 .ToImmutableArray();
 
             if (fixKind == DiagnosticFixKind.CompilerError)