diff --git a/clang/lib/Lex/ModuleMap.cpp b/clang/lib/Lex/ModuleMap.cpp
--- a/clang/lib/Lex/ModuleMap.cpp
+++ b/clang/lib/Lex/ModuleMap.cpp
@@ -1303,9 +1303,16 @@
   // Canonicalize the directory.
   StringRef CanonicalDir = FM.getCanonicalName(*DirEntry);
   if (CanonicalDir != Dir) {
-    bool Done = llvm::sys::path::replace_path_prefix(Path, Dir, CanonicalDir);
-    (void)Done;
-    assert(Done && "Path should always start with Dir");
+    auto CanonicalDirEntry = FM.getDirectory(CanonicalDir);
+    // Only use the canonicalized path if it resolves to the same entry as the
+    // original. This is not true if there's a VFS overlay on top of a FS where
+    // the directory is a symlink. The overlay would not remap the target path
+    // of the symlink to the same directory entry in that case.
+    if (CanonicalDirEntry && *CanonicalDirEntry == *DirEntry) {
+      bool Done = llvm::sys::path::replace_path_prefix(Path, Dir, CanonicalDir);
+      (void)Done;
+      assert(Done && "Path should always start with Dir");
+    }
   }
 
   // In theory, the filename component should also be canonicalized if it
diff --git a/clang/test/ClangScanDeps/modules-symlink-dir-vfs.c b/clang/test/ClangScanDeps/modules-symlink-dir-vfs.c
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/modules-symlink-dir-vfs.c
@@ -0,0 +1,90 @@
+// This test checks that we're not canonicalizing framework directories that
+// play a role in VFS remapping. This could lead header search to fail when
+// building that module.
+
+// RUN: rm -rf %t
+// RUN: split-file %s %t
+
+// REQUIRES: shell
+
+// RUN: mkdir -p %t/frameworks-symlink
+// RUN: ln -s %t/frameworks/FW.framework %t/frameworks-symlink/FW.framework
+
+// RUN: mkdir -p %t/copy
+// RUN: cp %t/frameworks/FW.framework/Headers/FW.h     %t/copy
+// RUN: cp %t/frameworks/FW.framework/Headers/Header.h %t/copy
+
+//--- frameworks/FW.framework/Modules/module.modulemap
+framework module FW { umbrella header "FW.h" }
+//--- frameworks/FW.framework/Headers/FW.h
+#import <FW/Header.h>
+//--- frameworks/FW.framework/Headers/Header.h
+// empty
+
+//--- tu.m
+@import FW;
+
+//--- overlay.json.template
+{
+  "version": 0,
+  "case-sensitive": "false",
+  "roots": [
+    {
+      "contents": [
+        {
+          "external-contents": "DIR/copy/Header.h",
+          "name": "Header.h",
+          "type": "file"
+        },
+        {
+          "external-contents": "DIR/copy/FW.h",
+          "name": "FW.h",
+          "type": "file"
+        }
+      ],
+      "name": "DIR/frameworks-symlink/FW.framework/Headers",
+      "type": "directory"
+    }
+  ]
+}
+
+//--- cdb.json.template
+[{
+  "directory": "DIR",
+  "file": "DIR/tu.m",
+  "command": "clang -fmodules -fmodules-cache-path=DIR/cache -ivfsoverlay DIR/overlay.json -F DIR/frameworks-symlink -c DIR/tu.m -o DIR/tu.o -Werror=non-modular-include-in-framework-module"
+}]
+
+// RUN: sed -e "s|DIR|%/t|g" %t/cdb.json.template > %t/cdb.json
+// RUN: sed -e "s|DIR|%/t|g" %t/overlay.json.template > %t/overlay.json
+
+// RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full > %t/result.json
+// RUN: cat %t/result.json | sed 's:\\\\\?:/:g' | FileCheck %s -DPREFIX=%/t
+
+// CHECK:      {
+// CHECK-NEXT:   "modules": [
+// CHECK-NEXT:     {
+// CHECK-NEXT:       "clang-module-deps": [],
+// CHECK-NEXT:       "clang-modulemap-file": "[[PREFIX]]/frameworks-symlink/FW.framework/Modules/module.modulemap",
+// CHECK-NEXT:       "command-line": [
+// CHECK-NEXT:         "-cc1",
+// CHECK:              "-emit-module",
+// CHECK-NEXT:         "-x",
+// CHECK-NEXT:         "objective-c",
+// CHECK-NEXT:         "[[PREFIX]]/frameworks-symlink/FW.framework/Modules/module.modulemap",
+// CHECK:            ],
+// CHECK-NEXT:       "context-hash": "{{.*}}",
+// CHECK-NEXT:       "file-deps": [
+// CHECK-NEXT:         "[[PREFIX]]/copy/FW.h",
+// CHECK-NEXT:         "[[PREFIX]]/copy/Header.h",
+// CHECK-NEXT:         "[[PREFIX]]/frameworks-symlink/FW.framework/Modules/module.modulemap"
+// CHECK-NEXT:       ],
+// CHECK-NEXT:       "name": "FW"
+// CHECK-NEXT:     }
+// CHECK-NEXT:   ],
+// CHECK-NEXT:   "translation-units": [
+// CHECK:        ]
+// CHECK:      }
+
+// RUN: %deps-to-rsp %t/result.json --module-name=FW > %t/FW.cc1.rsp
+// RUN: %clang @%t/FW.cc1.rsp