diff --git a/go/extractor/BUILD.bazel b/go/extractor/BUILD.bazel
index 23158e25b15..c8e66c98d21 100644
--- a/go/extractor/BUILD.bazel
+++ b/go/extractor/BUILD.bazel
@@ -19,6 +19,7 @@ go_library(
         "//go/extractor/dbscheme",
         "//go/extractor/diagnostics",
         "//go/extractor/srcarchive",
+        "//go/extractor/subst",
         "//go/extractor/toolchain",
         "//go/extractor/trap",
         "//go/extractor/util",
diff --git a/go/extractor/extractor.go b/go/extractor/extractor.go
index 158f0029704..e3d134a522d 100644
--- a/go/extractor/extractor.go
+++ b/go/extractor/extractor.go
@@ -25,6 +25,7 @@ import (
 	"github.com/github/codeql-go/extractor/dbscheme"
 	"github.com/github/codeql-go/extractor/diagnostics"
 	"github.com/github/codeql-go/extractor/srcarchive"
+	"github.com/github/codeql-go/extractor/subst"
 	"github.com/github/codeql-go/extractor/toolchain"
 	"github.com/github/codeql-go/extractor/trap"
 	"github.com/github/codeql-go/extractor/util"
@@ -764,9 +765,9 @@ 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 subst.ResolvePath(path)
 }
 
 // extractFile extracts AST information for the given file
diff --git a/go/extractor/subst/BUILD.bazel b/go/extractor/subst/BUILD.bazel
new file mode 100644
index 00000000000..a1975f3312a
--- /dev/null
+++ b/go/extractor/subst/BUILD.bazel
@@ -0,0 +1,18 @@
+load("@rules_go//go:def.bzl", "go_library", "go_test")
+
+go_library(
+    name = "subst",
+    srcs = [
+        "subst.go",
+        "subst_other.go",
+        "subst_windows.go",
+    ],
+    importpath = "github.com/github/codeql-go/extractor/subst",
+    visibility = ["//go:__subpackages__"],
+)
+
+go_test(
+    name = "subst_test",
+    srcs = ["subst_test.go"],
+    embed = [":subst"],
+)
diff --git a/go/extractor/subst/subst.go b/go/extractor/subst/subst.go
new file mode 100644
index 00000000000..885f9f09a81
--- /dev/null
+++ b/go/extractor/subst/subst.go
@@ -0,0 +1,30 @@
+package subst
+
+// 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 {
+	return resolvePath(path, ResolveDrive)
+}
+
+func resolvePath(path string, resolveDrive func(string) 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 := resolveDrive(path[:3])
+	if resolved == "" {
+		return path
+	}
+	return resolved + path[2:]
+}
diff --git a/go/extractor/subst/subst_other.go b/go/extractor/subst/subst_other.go
new file mode 100644
index 00000000000..8e153bf3bd6
--- /dev/null
+++ b/go/extractor/subst/subst_other.go
@@ -0,0 +1,6 @@
+//go:build !windows
+
+package subst
+
+// ResolveDrive is a no-op on non-Windows platforms.
+func ResolveDrive(driveRoot string) string { return "" }
diff --git a/go/extractor/subst/subst_test.go b/go/extractor/subst/subst_test.go
new file mode 100644
index 00000000000..28a23849a8a
--- /dev/null
+++ b/go/extractor/subst/subst_test.go
@@ -0,0 +1,86 @@
+package subst
+
+import "testing"
+
+func TestResolvePath(t *testing.T) {
+	t.Parallel()
+
+	tests := []struct {
+		name        string
+		path        string
+		resolveRoot string
+		resolved    string
+		expected    string
+	}{
+		{
+			name:        "resolved backslash path",
+			path:        `X:\dir\file.go`,
+			resolveRoot: `X:\`,
+			resolved:    `C:\target`,
+			expected:    `C:\target\dir\file.go`,
+		},
+		{
+			name:        "resolved slash path",
+			path:        `X:/dir/file.go`,
+			resolveRoot: `X:/`,
+			resolved:    `C:\target`,
+			expected:    `C:\target/dir/file.go`,
+		},
+		{
+			name:        "lowercase drive letter",
+			path:        `x:\dir\file.go`,
+			resolveRoot: `x:\`,
+			resolved:    `C:\target`,
+			expected:    `C:\target\dir\file.go`,
+		},
+		{
+			name:     "unresolved drive",
+			path:     `X:\dir\file.go`,
+			resolveRoot: `X:\`,
+			expected: `X:\dir\file.go`,
+		},
+		{
+			name:     "relative path",
+			path:     `dir\file.go`,
+			expected: `dir\file.go`,
+		},
+		{
+			name:     "non drive prefix",
+			path:     `\\server\share\file.go`,
+			expected: `\\server\share\file.go`,
+		},
+		{
+			name:     "missing separator after colon",
+			path:     `X:file.go`,
+			expected: `X:file.go`,
+		},
+	}
+
+	for _, test := range tests {
+		test := test
+		t.Run(test.name, func(t *testing.T) {
+			t.Parallel()
+
+			resolveCalls := 0
+			actual := resolvePath(test.path, func(driveRoot string) string {
+				resolveCalls++
+				if driveRoot != test.resolveRoot {
+					t.Fatalf("resolvePath passed drive root %q, want %q", driveRoot, test.resolveRoot)
+				}
+				return test.resolved
+			})
+
+			if actual != test.expected {
+				t.Fatalf("resolvePath(%q) = %q, want %q", test.path, actual, test.expected)
+			}
+
+			wantCalls := 0
+			if test.resolveRoot != "" {
+				wantCalls = 1
+			}
+			if resolveCalls != wantCalls {
+				t.Fatalf("resolvePath(%q) made %d resolve calls, want %d", test.path, resolveCalls, wantCalls)
+			}
+		})
+	}
+}
diff --git a/go/extractor/subst/subst_windows.go b/go/extractor/subst/subst_windows.go
new file mode 100644
index 00000000000..cb6a60984c0
--- /dev/null
+++ b/go/extractor/subst/subst_windows.go
@@ -0,0 +1,67 @@
+//go:build windows
+
+package subst
+
+import (
+	"os"
+	"path/filepath"
+	"syscall"
+	"unsafe"
+)
+
+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
+}
+
+// ResolveDrive resolves a subst'd drive root (e.g. "X:\") to its backing path.
+// Returns "" if the drive is not subst'd or on error.
+func ResolveDrive(driveRoot string) string {
+	if !available {
+		return ""
+	}
+	driveBytes := append([]byte(driveRoot), 0)
+	ret, _, _ := procResolve.Call(uintptr(unsafe.Pointer(&driveBytes[0])))
+	if ret == 0 {
+		return ""
+	}
+	result := goString((*byte)(unsafe.Pointer(ret)))
+	if procFree != nil {
+		procFree.Call(ret)
+	}
+	return result
+}
+
+func goString(p *byte) string {
+	if p == nil {
+		return ""
+	}
+	var n int
+	for ptr := unsafe.Pointer(p); *(*byte)(ptr) != 0; n++ {
+		ptr = unsafe.Add(ptr, 1)
+	}
+	return string(unsafe.Slice(p, n))
+}
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 79ce2d8d8d3..974a72be4b0 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 class FileUtil
 	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 00000000000..f7cf6364b64
--- /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;
+	}
+}