diff --git a/SamplesDef.json b/SamplesDef.json
index 941ce2d04..ca806929e 100644
--- a/SamplesDef.json
+++ b/SamplesDef.json
@@ -143,6 +143,20 @@
                 "&'./{testFolder}/projects/output/win64/{configuration}/fastbuildsimpleexecutable.exe'"
             ]
         },
+        {
+            "Name": "FastBuildDuplicateFile",
+            "CIs": [ "github", "gitlab" ],
+            "OSs": [ "windows-2019", "windows-2022" ],
+            "Frameworks": [ "net6.0" ],
+            "Configurations": [ "debug", "release" ],
+            "TestFolder": "samples/FastBuildDuplicateFile",
+            "Commands":
+            [
+                "./RunSharpmake.ps1 -workingDirectory {testFolder} -sharpmakeFile \"FastBuildDuplicateFile.sharpmake.cs\" -framework {framework}",
+                "./Compile.ps1 -slnOrPrjFile \"fastbuildsample_{VsVersionSuffix}_win64_fastbuild.sln\" -configuration {configuration} -platform \"x64\" -WorkingDirectory \"{testFolder}/projects\" -VsVersion {os} -compiler MsBuild",
+                "&'./{testFolder}/projects/output/win64/{configuration}/duplicatefileproject.exe'"
+            ]
+        },
         {
             "Name": "HelloAndroid",
             "CIs": [],
diff --git a/Sharpmake.Generators/FastBuild/Bff.Template.cs b/Sharpmake.Generators/FastBuild/Bff.Template.cs
index b8536eda7..9056b8cdd 100644
--- a/Sharpmake.Generators/FastBuild/Bff.Template.cs
+++ b/Sharpmake.Generators/FastBuild/Bff.Template.cs
@@ -290,6 +290,7 @@ public static class ConfigurationFile
     .CompilerInputPattern     = [fastBuildCompilerInputPattern]
     .CompilerInputExcludedFiles = [fastBuildInputExcludedFiles]
     .CompilerInputFiles       = [fastBuildSourceFiles]
+    .CompilerInputFilesRoot   = '[fastBuildInputFilesRootPath]'
 
 ";
 
diff --git a/Sharpmake.Generators/FastBuild/Bff.cs b/Sharpmake.Generators/FastBuild/Bff.cs
index b92b6863a..ae8815c75 100644
--- a/Sharpmake.Generators/FastBuild/Bff.cs
+++ b/Sharpmake.Generators/FastBuild/Bff.cs
@@ -1130,6 +1130,13 @@ List<string> skipFiles
                         fastBuildProjectDependencies.Add("[fastBuildOutputFileShortName]_objects");
                         string fastBuildObjectListEmbeddedResources = FormatListPartForTag(embeddedResourceFilesSections, 32, true);
 
+                        string fastBuildInputFilesRootPath = FileGeneratorUtilities.RemoveLineTag;
+
+                        if (conf.FastBuildInputFilesRootPath != null)
+                        {
+                            fastBuildInputFilesRootPath = CurrentBffPathKeyCombine(Util.PathGetRelative(context.ProjectDirectory, conf.FastBuildInputFilesRootPath));
+                        }
+
                         using (bffGenerator.Declare("conf", conf))
                         using (bffGenerator.Declare("project", project))
                         using (bffGenerator.Declare("target", conf.Target))
@@ -1170,6 +1177,7 @@ List<string> skipFiles
                                     using (bffGenerator.Declare("fastBuildLibrarianAdditionalInputs", librarianAdditionalInputs))
                                     using (bffGenerator.Declare("fastBuildCompileAsC", fastBuildCompileAsC))
                                     using (bffGenerator.Declare("fastBuildUnityName", fastBuildUnityName ?? FileGeneratorUtilities.RemoveLineTag))
+                                    using (bffGenerator.Declare("fastBuildInputFilesRootPath", fastBuildInputFilesRootPath))
                                     using (bffGenerator.Declare("fastBuildClangFileLanguage", clangFileLanguage))
                                     using (bffGenerator.Declare("fastBuildDeoptimizationWritableFiles", fastBuildDeoptimizationWritableFiles))
                                     using (bffGenerator.Declare("fastBuildDeoptimizationWritableFilesWithToken", fastBuildDeoptimizationWritableFilesWithToken))
diff --git a/Sharpmake/Project.Configuration.cs b/Sharpmake/Project.Configuration.cs
index b0a6cb580..382653671 100644
--- a/Sharpmake/Project.Configuration.cs
+++ b/Sharpmake/Project.Configuration.cs
@@ -1544,6 +1544,8 @@ public string FastBuildUnityPath
                 set { _fastBuildUnityPath = value; }
             }
 
+            public string FastBuildInputFilesRootPath = null;
+
             /// <summary>
             /// If specified, overrides <c>Project.DefaultBlobWorkFileHeader</c>.
             /// </summary>
diff --git a/samples/FastBuildDuplicateFile/FastBuildDuplicateFile.sharpmake.cs b/samples/FastBuildDuplicateFile/FastBuildDuplicateFile.sharpmake.cs
new file mode 100644
index 000000000..2f5d2afdf
--- /dev/null
+++ b/samples/FastBuildDuplicateFile/FastBuildDuplicateFile.sharpmake.cs
@@ -0,0 +1,124 @@
+// Copyright (c) Ubisoft. All Rights Reserved.
+// Licensed under the Apache 2.0 License. See LICENSE.md in the project root for license information.
+
+using System.IO;
+using Sharpmake;
+
+namespace FastBuildDuplicateFile
+{
+    public static class Globals
+    {
+        // branch root path relative to current sharpmake file location
+        public const string RelativeRootPath = @".\codebase";
+        public static string RootDirectory;
+    }
+
+    [Sharpmake.Generate]
+    public class DuplicateFileProject : Project
+    {
+        public DuplicateFileProject()
+        {
+            Name = "DuplicateFileProject";
+
+            StripFastBuildSourceFiles = false;
+
+            AddTargets(new Target(
+                        Platform.win64,
+                        DevEnv.vs2019 | DevEnv.vs2022,
+                        Optimization.Debug | Optimization.Release,
+                        OutputType.Lib,
+                        Blob.NoBlob,
+                        BuildSystem.FastBuild | BuildSystem.MSBuild
+            ));
+
+            SourceRootPath = @"[project.SharpmakeCsPath]\codebase";
+        }
+
+        [Configure()]
+        public void ConfigureAll(Configuration conf, Target target)
+        {
+            conf.ProjectFileName = "[project.Name]_[target.DevEnv]_[target.Platform]_[target.BuildSystem]";
+            conf.ProjectPath = @"[project.SharpmakeCsPath]\projects";
+            conf.Options.Add(Options.Vc.Compiler.Exceptions.Enable);
+        }
+
+        [Configure(BuildSystem.FastBuild)]
+        public void ConfigureFastBuild(Configuration conf, Target target)
+        {
+            conf.IsFastBuild = true;
+            conf.FastBuildBlobbed = target.Blob == Blob.FastBuildUnitys;
+            conf.FastBuildInputFilesRootPath = SourceRootPath;
+
+            // Force writing to pdb from different cl.exe process to go through the pdb server
+            conf.AdditionalCompilerOptions.Add("/FS");
+        }
+
+        [Configure(Optimization.Release)]
+        public virtual void ConfigureRelease(Configuration conf, Target target)
+        {
+            // Testing generation of what is needed for working fastbuild deoptimization when using non-exposed compiler optimization options.
+            conf.AdditionalCompilerOptimizeOptions.Add("/O2"); // This switch is known but for the purpose of this test we will put in in this field.
+            conf.AdditionalCompilerOptimizeOptions.Add("/Os"); // This switch is known but for the purpose of this test we will put in in this field.
+            conf.AdditionalCompilerOptions.Add("/bigobj");
+            conf.FastBuildDeoptimization = Configuration.DeoptimizationWritableFiles.DeoptimizeWritableFiles;
+        }
+    }
+
+    [Sharpmake.Generate]
+    public class DuplicateFileSolution : Sharpmake.Solution
+    {
+        public DuplicateFileSolution()
+        {
+            Name = "FastBuildSample";
+
+            AddTargets(new Target(
+                        Platform.win64,
+                        DevEnv.vs2019 | DevEnv.vs2022,
+                        Optimization.Debug | Optimization.Release,
+                        OutputType.Lib,
+                        Blob.NoBlob,
+                        BuildSystem.FastBuild | BuildSystem.MSBuild
+            ));
+        }
+
+        [Configure()]
+        public void ConfigureAll(Configuration conf, Target target)
+        {
+            conf.SolutionFileName = "[solution.Name]_[target.DevEnv]_[target.Platform]_[target.BuildSystem]";
+            conf.SolutionPath = @"[solution.SharpmakeCsPath]\projects";
+
+            conf.AddProject<DuplicateFileProject>(target);
+        }
+    }
+
+    public static class Main
+    {
+        private static void ConfigureRootDirectory()
+        {
+            FileInfo fileInfo = Util.GetCurrentSharpmakeFileInfo();
+            string rootDirectory = Path.Combine(fileInfo.DirectoryName, Globals.RelativeRootPath);
+            Globals.RootDirectory = Util.SimplifyPath(rootDirectory);
+        }
+
+        [Sharpmake.Main]
+        public static void SharpmakeMain(Sharpmake.Arguments arguments)
+        {
+            ConfigureRootDirectory();
+
+            // for the purpose of this sample, we'll reuse the FastBuild executable that live in the sharpmake source repo
+            string sharpmakeFastBuildDir = Util.PathGetAbsolute(Globals.RootDirectory, @"..\..\..\tools\FastBuild");
+            FastBuildSettings.FastBuildMakeCommand = Path.Combine(sharpmakeFastBuildDir, "Windows-x64", "FBuild.exe");
+
+            // This is necessary since there is no rc.exe in the same directory than link.exe
+            FastBuildSettings.SetPathToResourceCompilerInEnvironment = true;
+
+            // Add an additional environment variable for fastbuild for testing
+            FastBuildSettings.AdditionalGlobalEnvironmentVariables.Add("KEY", "VALUE");
+
+            KitsRootPaths.SetUseKitsRootForDevEnv(DevEnv.vs2019, KitsRootEnum.KitsRoot10, Options.Vc.General.WindowsTargetPlatformVersion.v10_0_19041_0);
+            KitsRootPaths.SetUseKitsRootForDevEnv(DevEnv.vs2022, KitsRootEnum.KitsRoot10, Options.Vc.General.WindowsTargetPlatformVersion.v10_0_19041_0);
+
+            arguments.Generate<DuplicateFileSolution>();
+        }
+    }
+}
diff --git a/samples/FastBuildDuplicateFile/codebase/main.cpp b/samples/FastBuildDuplicateFile/codebase/main.cpp
new file mode 100644
index 000000000..a577c11dd
--- /dev/null
+++ b/samples/FastBuildDuplicateFile/codebase/main.cpp
@@ -0,0 +1,10 @@
+#include <iostream>
+
+#include "test1/test.h"
+#include "test2/test.h"
+
+int main(int, char**)
+{
+    std::cout << "I have two files named test.h. test1 makes " << test1() << ". test2 makes " << test2() << "." << std::endl;
+    return 0;
+}
diff --git a/samples/FastBuildDuplicateFile/codebase/test1/test.cpp b/samples/FastBuildDuplicateFile/codebase/test1/test.cpp
new file mode 100644
index 000000000..087d52e37
--- /dev/null
+++ b/samples/FastBuildDuplicateFile/codebase/test1/test.cpp
@@ -0,0 +1,3 @@
+#include "test.h"
+
+int test1() { return 1; }
diff --git a/samples/FastBuildDuplicateFile/codebase/test1/test.h b/samples/FastBuildDuplicateFile/codebase/test1/test.h
new file mode 100644
index 000000000..39a74fa7f
--- /dev/null
+++ b/samples/FastBuildDuplicateFile/codebase/test1/test.h
@@ -0,0 +1,3 @@
+#pragma once
+
+int test1();
diff --git a/samples/FastBuildDuplicateFile/codebase/test2/test.cpp b/samples/FastBuildDuplicateFile/codebase/test2/test.cpp
new file mode 100644
index 000000000..e426e6690
--- /dev/null
+++ b/samples/FastBuildDuplicateFile/codebase/test2/test.cpp
@@ -0,0 +1,3 @@
+#include "test.h"
+
+int test2() { return 2; }
diff --git a/samples/FastBuildDuplicateFile/codebase/test2/test.h b/samples/FastBuildDuplicateFile/codebase/test2/test.h
new file mode 100644
index 000000000..512b315e3
--- /dev/null
+++ b/samples/FastBuildDuplicateFile/codebase/test2/test.h
@@ -0,0 +1,3 @@
+#pragma once
+
+int test2();
diff --git a/samples/Properties/launchSettings.json b/samples/Properties/launchSettings.json
index 23f49d383..3decf803c 100644
--- a/samples/Properties/launchSettings.json
+++ b/samples/Properties/launchSettings.json
@@ -54,6 +54,12 @@
       "commandLineArgs": "/sources(@'FastBuildSimpleExecutable.sharpmake.cs')",
       "workingDirectory": "$(ProjectDir)\\FastBuildSimpleExecutable"
     },
+    "Sample (FastBuildDuplicateFile)": {
+      "commandName": "Executable",
+      "executablePath": "$(ProjectDir)\\..\\Sharpmake.Application\\bin\\$(Configuration)\\$(TargetFramework)\\Sharpmake.Application.exe",
+      "commandLineArgs": "/sources(@'FastBuildDuplicateFile.sharpmake.cs')",
+      "workingDirectory": "$(ProjectDir)\\FastBuildDuplicateFile"
+    },
     "Sample (HelloAndroid)": {
       "commandName": "Executable",
       "executablePath": "$(ProjectDir)\\..\\Sharpmake.Application\\bin\\$(Configuration)\\$(TargetFramework)\\Sharpmake.Application.exe",