diff --git a/mypy/build.py b/mypy/build.py
index 7c3f16704c5a..7fe59b351a6b 100644
--- a/mypy/build.py
+++ b/mypy/build.py
@@ -674,6 +674,7 @@ def __init__(
             if options.custom_typeshed_dir is not None:
                 # Check if module lives under custom_typeshed_dir subtree
                 custom_typeshed_dir = os.path.abspath(options.custom_typeshed_dir)
+                path = os.path.abspath(path)
                 if os.path.commonpath((path, custom_typeshed_dir)) == custom_typeshed_dir:
                     continue
 
diff --git a/test-data/unit/cmdline.test b/test-data/unit/cmdline.test
index ea1e9cba165a..97a9dcaa7410 100644
--- a/test-data/unit/cmdline.test
+++ b/test-data/unit/cmdline.test
@@ -1465,3 +1465,16 @@ sys.path = path
 mypy: "typing.py" shadows library module "typing"
 note: A user-defined top-level module with name "typing" is not supported
 == Return code: 2
+
+[case testCustomTypeshedDirWithRelativePathDoesNotCrash]
+# cmd: mypy --custom-typeshed-dir dir dir/typing.pyi
+[file dir/stdlib/abc.pyi]
+[file dir/stdlib/builtins.pyi]
+[file dir/stdlib/sys.pyi]
+[file dir/stdlib/types.pyi]
+[file dir/stdlib/typing.pyi]
+[file dir/stdlib/typing_extensions.pyi]
+[file dir/stdlib/VERSIONS]
+[out]
+Failed to find builtin module mypy_extensions, perhaps typeshed is broken?
+== Return code: 2