diff --git a/lib/ex_doc/autolink.ex b/lib/ex_doc/autolink.ex
index 8fa342b70..fb9697ed4 100644
--- a/lib/ex_doc/autolink.ex
+++ b/lib/ex_doc/autolink.ex
@@ -156,10 +156,16 @@ defmodule ExDoc.Autolink do
   def maybe_warn(config, ref, visibility, metadata) do
     file = Path.relative_to_cwd(config.file)
 
-    unless Enum.any?(
-             [config.id, config.module_id, file],
-             config.skip_undefined_reference_warnings_on
-           ) do
+    skip_checks =
+      case metadata do
+        %{file_path: file_path} when is_binary(file_path) ->
+          [config.id, config.module_id, file, file_path]
+
+        _ ->
+          [config.id, config.module_id, file]
+      end
+
+    if not Enum.any?(skip_checks, config.skip_undefined_reference_warnings_on) do
       warn(config, ref, visibility, metadata)
     end
   end
diff --git a/test/ex_doc/language/elixir_test.exs b/test/ex_doc/language/elixir_test.exs
index 4023708c1..704c51d8d 100644
--- a/test/ex_doc/language/elixir_test.exs
+++ b/test/ex_doc/language/elixir_test.exs
@@ -644,6 +644,30 @@ defmodule ExDoc.Language.ElixirTest do
                       ~s|<a href="Foo Bar.md">Foo</a>|
            end) =~ ~s|documentation references file "Foo Bar.md" but it does not exist|
 
+    # skip_undefined_reference_warnings_on matches file_path (without fragment)
+    refute_warn(fn ->
+      assert autolink_doc(
+               "[Foo](Foo Bar.md)",
+               opts ++
+                 [
+                   extras: %{},
+                   skip_undefined_reference_warnings_on: &(&1 == "Foo Bar.md")
+                 ]
+             ) == ~s|<a href="Foo Bar.md">Foo</a>|
+    end)
+
+    # skip_undefined_reference_warnings_on matches file_path even with fragment
+    refute_warn(fn ->
+      autolink_doc(
+        "[Foo](Foo Bar.md#section)",
+        opts ++
+          [
+            extras: %{},
+            skip_undefined_reference_warnings_on: &(&1 == "Foo Bar.md")
+          ]
+      )
+    end)
+
     assert warn(fn ->
              assert autolink_doc("[Bar A](`Bar.A`)", opts) == "Bar A"
            end) =~ ~s|module "Bar.A" but it is undefined|
@@ -718,6 +742,12 @@ defmodule ExDoc.Language.ElixirTest do
     message
   end
 
+  defp refute_warn(fun) when is_function(fun, 0) do
+    fun.()
+
+    refute_received {:warn, _, _}
+  end
+
   defp autolink_spec(spec, options \\ []) do
     config = struct!(ExDoc.Autolink, Keyword.merge(@default_options, options))
     ExDoc.Language.Elixir.autolink_spec(spec, config)