diff --git a/go/extractor/extractor.go b/go/extractor/extractor.go
index 158f0029704d..8310a97c56b7 100644
--- a/go/extractor/extractor.go
+++ b/go/extractor/extractor.go
@@ -764,9 +764,9 @@ func normalizedPath(ast *ast.File, fset *token.FileSet) string {
 	file := fset.File(ast.Package).Name()
 	path, err := filepath.EvalSymlinks(file)
 	if err != nil {
-		return file
+		path = file
 	}
-	return path
+	return util.ResolvePath(path)
 }
 
 // extractFile extracts AST information for the given file
diff --git a/go/extractor/go.mod b/go/extractor/go.mod
index cea20f1bd4a4..e7d35a8c0843 100644
--- a/go/extractor/go.mod
+++ b/go/extractor/go.mod
@@ -13,7 +13,10 @@ require (
 	golang.org/x/tools v0.47.0
 )
 
-require github.com/stretchr/testify v1.11.1
+require (
+	github.com/stretchr/testify v1.11.1
+	golang.org/x/sys v0.46.0
+)
 
 require (
 	github.com/davecgh/go-spew v1.1.1 // indirect
diff --git a/go/extractor/go.sum b/go/extractor/go.sum
index a928a105f684..5cba90917b2f 100644
--- a/go/extractor/go.sum
+++ b/go/extractor/go.sum
@@ -10,6 +10,8 @@ golang.org/x/mod v0.37.0 h1:vF1DjpVEshcIqoEaauuHebaLk1O1forxjxBaVn884JQ=
 golang.org/x/mod v0.37.0/go.mod h1:m8S8VeM9r4dzDwjrKO0a1sZP3YjeMamRRlD+fmR2Q/0=
 golang.org/x/sync v0.21.0 h1:HLII4xRRTtCRkxYp4HNFF0Js/Og6q2i++KXbg0gHCwM=
 golang.org/x/sync v0.21.0/go.mod h1:9xrNwdLfx4jkKbNva9FpL6vEN7evnE43NNNJQ2LF3+0=
+golang.org/x/sys v0.46.0 h1:noSf2Fq6F8DBgS+LysIkx7rIExoNHJsxOAtPp4rthXw=
+golang.org/x/sys v0.46.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
 golang.org/x/tools v0.47.0 h1:7Kn5x/d1svx/PzryTsqeoZN4TZwqeH5pGWjefhLi/1Q=
 golang.org/x/tools v0.47.0/go.mod h1:dFHnyTvFWY212G+h7ZY4Vsp/K3U4/7W9TyVaAul8uCA=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM=
diff --git a/go/extractor/util/BUILD.bazel b/go/extractor/util/BUILD.bazel
index ccebf5ebd865..5735e65cf9f4 100644
--- a/go/extractor/util/BUILD.bazel
+++ b/go/extractor/util/BUILD.bazel
@@ -9,11 +9,18 @@ go_library(
         "logging.go",
         "overlays.go",
         "semver.go",
+        "subst_other.go",
+        "subst_windows.go",
         "util.go",
     ],
     importpath = "github.com/github/codeql-go/extractor/util",
     visibility = ["//visibility:public"],
-    deps = ["@org_golang_x_mod//semver"],
+    deps = ["@org_golang_x_mod//semver"] + select({
+        "@rules_go//go/platform:windows": [
+            "@org_golang_x_sys//windows",
+        ],
+        "//conditions:default": [],
+    }),
 )
 
 go_test(
diff --git a/go/extractor/util/subst_other.go b/go/extractor/util/subst_other.go
new file mode 100644
index 000000000000..b32420a7746e
--- /dev/null
+++ b/go/extractor/util/subst_other.go
@@ -0,0 +1,6 @@
+//go:build !windows
+
+package util
+
+// ResolvePath is a no-op on non-Windows platforms.
+func ResolvePath(path string) string { return path }
diff --git a/go/extractor/util/subst_windows.go b/go/extractor/util/subst_windows.go
new file mode 100644
index 000000000000..c6c5efc68a43
--- /dev/null
+++ b/go/extractor/util/subst_windows.go
@@ -0,0 +1,86 @@
+//go:build windows
+
+package util
+
+import (
+	"os"
+	"path/filepath"
+	"syscall"
+	"unsafe"
+
+	"golang.org/x/sys/windows"
+)
+
+var (
+	dll         *syscall.DLL
+	procResolve *syscall.Proc
+	procFree    *syscall.Proc
+	available   bool
+)
+
+func init() {
+	dist := os.Getenv("CODEQL_DIST")
+	if dist == "" {
+		return
+	}
+	dllPath := filepath.Join(dist, "tools", "win64", "canonicalize.dll")
+	d, err := syscall.LoadDLL(dllPath)
+	if err != nil {
+		return
+	}
+	p, err := d.FindProc("resolve_subst_u8")
+	if err != nil {
+		return
+	}
+	f, _ := d.FindProc("resolve_subst_free_u8")
+	dll = d
+	procResolve = p
+	procFree = f
+	available = true
+}
+
+// ResolvePath resolves subst'd drive letters in a full path.
+// If the path starts with a subst'd drive letter, replaces it with the backing path.
+// Otherwise returns the path unchanged.
+func ResolvePath(path string) string {
+	if len(path) < 3 {
+		return path
+	}
+	if path[1] != ':' {
+		return path
+	}
+	if path[2] != '\\' && path[2] != '/' {
+		return path
+	}
+	c := path[0]
+	if !((c >= 'A' && c <= 'Z') || (c >= 'a' && c <= 'z')) {
+		return path
+	}
+
+	resolved, ok := resolveDrive(path[:3])
+	if !ok {
+		return path
+	}
+	return resolved + path[2:]
+}
+
+// resolveDrive resolves a subst'd drive root (e.g. "X:\") to its backing path.
+// The second return value is false if the drive is not subst'd or on error.
+func resolveDrive(driveRoot string) (string, bool) {
+	if !available {
+		return "", false
+	}
+	driveBytes, err := windows.ByteSliceFromString(driveRoot)
+	if err != nil {
+		return "", false
+	}
+	ret, _, _ := procResolve.Call(uintptr(unsafe.Pointer(&driveBytes[0])))
+	if ret == 0 {
+		return "", false
+	}
+	result := windows.BytePtrToString((*byte)(unsafe.Pointer(ret)))
+	if procFree != nil {
+		procFree.Call(ret)
+	}
+	return result, true
+}
diff --git a/java/kotlin-extractor/src/main/java/com/semmle/util/files/FileUtil.java b/java/kotlin-extractor/src/main/java/com/semmle/util/files/FileUtil.java
index 79ce2d8d8d3d..974a72be4b06 100644
--- a/java/kotlin-extractor/src/main/java/com/semmle/util/files/FileUtil.java
+++ b/java/kotlin-extractor/src/main/java/com/semmle/util/files/FileUtil.java
@@ -1242,12 +1242,13 @@ public static String relativePathLink (File f, File base)
 	public static File tryMakeCanonical (File f)
 	{
 		try {
-			return f.getCanonicalFile();
+			f = f.getCanonicalFile();
 		}
 		catch (IOException ignored) {
 			Exceptions.ignore(ignored, "Can't log error: Could be too verbose.");
-			return new File(simplifyPath(f));
+			f = new File(simplifyPath(f));
 		}
+		return SubstResolver.resolve(f);
 	}
 
 
diff --git a/java/kotlin-extractor/src/main/java/com/semmle/util/files/SubstResolver.java b/java/kotlin-extractor/src/main/java/com/semmle/util/files/SubstResolver.java
new file mode 100644
index 000000000000..f7cf6364b64e
--- /dev/null
+++ b/java/kotlin-extractor/src/main/java/com/semmle/util/files/SubstResolver.java
@@ -0,0 +1,76 @@
+package com.semmle.util.files;
+
+import java.io.File;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+/**
+ * Resolves Windows {@code subst}ed drive letters to their underlying paths. On non-Windows
+ * platforms, or when the native library failed to load, {@link #resolve(File)} is a no-op that
+ * returns its argument unchanged.
+ */
+public class SubstResolver {
+	private static final boolean available;
+
+	static {
+		boolean loaded = false;
+		if (File.separatorChar == '\\') {
+			String dist = System.getenv("CODEQL_DIST");
+			if (dist != null && !dist.isEmpty()) {
+				try {
+					Path library = Paths.get(dist).resolve("tools").resolve("win64")
+							.resolve("canonicalize.dll").toAbsolutePath();
+					System.load(library.toString());
+					loaded = true;
+				} catch (RuntimeException | UnsatisfiedLinkError ignored) {
+				}
+			}
+		}
+		available = loaded;
+	}
+
+	private SubstResolver() {}
+
+	/**
+	 * Given a drive root like {@code "X:\\"}, returns the path that drive is
+	 * {@code subst}ed to, or {@code null} if the letter isn't a subst mapping.
+	 */
+	private static native String nativeResolveSubst(String driveRoot);
+
+	/**
+	 * If {@code f} is an absolute path starting with a {@code subst}ed drive letter, return an
+	 * equivalent path with the drive letter replaced by its target. Otherwise return {@code f}
+	 * unchanged.
+	 */
+	public static File resolve(File f) {
+		if (!available) {
+			return f;
+		}
+		String path = f.getPath();
+		if (path.length() < 3 || path.charAt(1) != ':') {
+			return f;
+		}
+		char sep = path.charAt(2);
+		if (sep != '\\' && sep != '/') {
+			return f;
+		}
+		if (!isDriveLetter(path.charAt(0))) {
+			return f;
+		}
+
+		String resolved = nativeResolveSubst(path.substring(0, 3));
+		if (resolved == null) {
+			return f;
+		}
+
+		return new File(resolved + path.substring(2));
+	}
+
+	private static boolean isDriveLetter(char c) {
+		return (c >= 'A' && c <= 'Z') || (c >= 'a' && c <= 'z');
+	}
+
+	public static boolean isAvailable() {
+		return available;
+	}
+}