diff --git a/src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs b/src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs
index ddd68ad109f5..ac292e837c8a 100644
--- a/src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs
+++ b/src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs
@@ -1412,9 +1412,12 @@ public static void WriteProjectFile(
         {
             Debug.Assert(targetFilePath is not null);
 
+            // Only add explicit Compile item when EnableDefaultCompileItems is not true.
+            // When EnableDefaultCompileItems=true, the file is included via default MSBuild globbing.
+            // See https://github.com/dotnet/sdk/issues/51785
             writer.WriteLine($"""
                   <ItemGroup>
-                    <Compile Include="{EscapeValue(targetFilePath)}" />
+                    <Compile Condition="'$(EnableDefaultCompileItems)' != 'true'" Include="{EscapeValue(targetFilePath)}" />
                   </ItemGroup>
 
                 """);
diff --git a/test/dotnet.Tests/CommandTests/Run/RunFileTests.cs b/test/dotnet.Tests/CommandTests/Run/RunFileTests.cs
index 1eebfddaef95..774e917d814d 100644
--- a/test/dotnet.Tests/CommandTests/Run/RunFileTests.cs
+++ b/test/dotnet.Tests/CommandTests/Run/RunFileTests.cs
@@ -726,6 +726,7 @@ public void ClassLibrary_EntryPointFileDoesNotExist()
 
     /// <summary>
     /// Other files in the folder are not part of the compilation.
+    /// See <see href="https://github.com/dotnet/sdk/issues/51785"/>.
     /// </summary>
     [Fact]
     public void MultipleFiles_RunEntryPoint()
@@ -750,9 +751,32 @@ public void MultipleFiles_RunEntryPoint()
             .WithWorkingDirectory(testInstance.Path)
             .Execute()
             .Should().Pass()
-            // warning CS2002: Source file 'Program.cs' specified multiple times
-            .And.HaveStdOutContaining("warning CS2002")
-            .And.HaveStdOutContaining("Hello, String from Util");
+            .And.HaveStdOut("Hello, String from Util");
+    }
+
+    /// <summary>
+    /// Setting EnableDefaultCompileItems=true via Directory.Build.props should not cause CS2002 warning.
+    /// See <see href="https://github.com/dotnet/sdk/issues/51785"/>.
+    /// </summary>
+    [Fact]
+    public void MultipleFiles_EnableDefaultCompileItemsViaDirectoryBuildProps()
+    {
+        var testInstance = _testAssetsManager.CreateTestDirectory();
+        File.WriteAllText(Path.Join(testInstance.Path, "Program.cs"), s_programDependingOnUtil);
+        File.WriteAllText(Path.Join(testInstance.Path, "Util.cs"), s_util);
+        File.WriteAllText(Path.Join(testInstance.Path, "Directory.Build.props"), """
+            <Project>
+                <PropertyGroup>
+                    <EnableDefaultCompileItems>true</EnableDefaultCompileItems>
+                </PropertyGroup>
+            </Project>
+            """);
+
+        new DotnetCommand(Log, "run", "Program.cs")
+            .WithWorkingDirectory(testInstance.Path)
+            .Execute()
+            .Should().Pass()
+            .And.HaveStdOut("Hello, String from Util");
     }
 
     /// <summary>
@@ -3941,7 +3965,7 @@ public void Api()
                       </ItemGroup>
 
                       <ItemGroup>
-                        <Compile Include="{programPath}" />
+                        <Compile Condition="'$(EnableDefaultCompileItems)' != 'true'" Include="{programPath}" />
                       </ItemGroup>
 
                       <ItemGroup>
@@ -4008,7 +4032,7 @@ public void Api_Diagnostic_01()
                       </PropertyGroup>
 
                       <ItemGroup>
-                        <Compile Include="{programPath}" />
+                        <Compile Condition="'$(EnableDefaultCompileItems)' != 'true'" Include="{programPath}" />
                       </ItemGroup>
 
                       <ItemGroup>
@@ -4078,7 +4102,7 @@ public void Api_Diagnostic_02()
                       </PropertyGroup>
 
                       <ItemGroup>
-                        <Compile Include="{programPath}" />
+                        <Compile Condition="'$(EnableDefaultCompileItems)' != 'true'" Include="{programPath}" />
                       </ItemGroup>
 
                       <ItemGroup>