diff --git a/compiler/src/dotty/tools/dotc/transform/PostTyper.scala b/compiler/src/dotty/tools/dotc/transform/PostTyper.scala
index 34bd406d69ba..3790691f05ec 100644
--- a/compiler/src/dotty/tools/dotc/transform/PostTyper.scala
+++ b/compiler/src/dotty/tools/dotc/transform/PostTyper.scala
@@ -335,7 +335,17 @@ class PostTyper extends MacroTransform with IdentityDenotTransformer { thisPhase
                && ctx.compilationUnit.source.exists
                && sym != defn.SourceFileAnnot
             then
-              sym.addAnnotation(Annotation.makeSourceFile(ctx.compilationUnit.source.file.path))
+              def sourcerootPath =
+                java.nio.file.Paths.get(ctx.settings.sourceroot.value)
+                .toAbsolutePath
+                .normalize
+              val file = ctx.compilationUnit.source.file
+              val jpath = file.jpath
+              val relativePath =
+                if jpath eq null then file.path // repl and other custom tests use abstract files with no path
+                else if jpath.isAbsolute then sourcerootPath.relativize(jpath.normalize).toString
+                else jpath.normalize.toString
+              sym.addAnnotation(Annotation.makeSourceFile(relativePath))
           else (tree.rhs, sym.info) match
             case (rhs: LambdaTypeTree, bounds: TypeBounds) =>
               VarianceChecker.checkLambda(rhs, bounds)
diff --git a/project/scripts/cmdTests b/project/scripts/cmdTests
index c3f3839b1c37..382c5a76de79 100755
--- a/project/scripts/cmdTests
+++ b/project/scripts/cmdTests
@@ -33,6 +33,11 @@ clear_out "$OUT"
 "$SBT" ";scalac -d $OUT/out.jar $SOURCE; scalac -decompile -color:never $OUT/out.jar" > "$tmp"
 grep -qe "def main(args: scala.Array\[scala.Predef.String\]): scala.Unit =" "$tmp"
 
+echo "testing that paths SourceFile annotations are relativized"
+clear_out "$OUT"
+"$SBT" ";scalac -d $OUT/out.jar $(pwd)/$SOURCE; scalac -decompile -color:never $OUT/out.jar" > "$tmp"
+grep -qe "SourceFile(\"$SOURCE\")" "$tmp"
+
 echo "testing sbt scalac with suspension"
 clear_out "$OUT"
 "$SBT" "scala3-compiler-bootstrapped/scalac -d $OUT tests/pos-macros/macros-in-same-project-1/Bar.scala tests/pos-macros/macros-in-same-project-1/Foo.scala"  > "$tmp"