diff --git a/python/packages/core/agent_framework/_skills.py b/python/packages/core/agent_framework/_skills.py
index 33d001b6f2..571c15ab7b 100644
--- a/python/packages/core/agent_framework/_skills.py
+++ b/python/packages/core/agent_framework/_skills.py
@@ -58,12 +58,13 @@
 )
 
 # Matches resource file references in skill markdown. Group 1 = relative file path.
-# Supports two forms:
-#   1. Markdown links: [text](path/file.ext)
-#   2. Backtick-quoted paths: `path/file.ext`
+# Only matches markdown links: [text](path/file.ext)
+# Backtick-quoted paths are intentionally excluded because backticks are standard
+# inline code formatting in markdown and do not imply the referenced file exists
+# in the skill directory.
 # Supports optional ./ or ../ prefixes; excludes URLs (no ":" in the path character class).
 _RESOURCE_LINK_RE = re.compile(
-    r"(?:\[.*?\]\(|`)(\.?\.?/?[\w][\w\-./]*\.\w+)(?:\)|`)",
+    r"\[.*?\]\((\.?\.?/?[\w][\w\-./]*\.\w+)\)",
 )
 
 # Matches YAML "key: value" lines. Group 1 = key, Group 2 = quoted value,
diff --git a/python/packages/core/tests/core/test_skills.py b/python/packages/core/tests/core/test_skills.py
index a77f214718..2fbcec608d 100644
--- a/python/packages/core/tests/core/test_skills.py
+++ b/python/packages/core/tests/core/test_skills.py
@@ -117,15 +117,17 @@ def test_ignores_urls(self) -> None:
     def test_empty_content(self) -> None:
         assert _extract_resource_paths("") == []
 
-    def test_extracts_backtick_quoted_paths(self) -> None:
+    def test_ignores_backtick_quoted_paths(self) -> None:
+        """Backtick-quoted filenames are standard markdown code formatting, not resource references."""
         content = "Use the template at `assets/template.md` and the script `./scripts/run.py`."
         paths = _extract_resource_paths(content)
-        assert paths == ["assets/template.md", "scripts/run.py"]
+        assert paths == []
 
-    def test_deduplicates_across_link_and_backtick(self) -> None:
+    def test_backtick_filenames_do_not_shadow_markdown_links(self) -> None:
+        """Markdown links are still extracted even when backtick filenames are present."""
         content = "See [doc](refs/FAQ.md) and also `refs/FAQ.md`."
         paths = _extract_resource_paths(content)
-        assert len(paths) == 1
+        assert paths == ["refs/FAQ.md"]
 
 
 class TestTryParseSkillDocument:
@@ -288,6 +290,18 @@ def test_excludes_skill_with_missing_resource(self, tmp_path: Path) -> None:
         skills = _discover_and_load_skills([str(tmp_path)])
         assert len(skills) == 0
 
+    def test_loads_skill_with_backtick_filenames_that_do_not_exist(self, tmp_path: Path) -> None:
+        """Backtick-quoted filenames should not be treated as resource references (issue #4369)."""
+        _write_skill(
+            tmp_path,
+            "my-skill",
+            body="Configure using `config.json` and `deploy.sh`.\nSee [prompt](prompt.jinja2) for the template.",
+            resources={"prompt.jinja2": "template content"},
+        )
+        skills = _discover_and_load_skills([str(tmp_path)])
+        assert "my-skill" in skills
+        assert skills["my-skill"].resource_names == ["prompt.jinja2"]
+
     def test_excludes_skill_with_path_traversal_resource(self, tmp_path: Path) -> None:
         _write_skill(
             tmp_path,