diff --git a/run_agent.py b/run_agent.py
index dc6c0e13d2..a7c583f61c 100644
--- a/run_agent.py
+++ b/run_agent.py
@@ -8266,6 +8266,7 @@ class AIAgent:
             model=self.model,
             messages=_msgs_for_chat,
             tools=self.tools,
+            base_url=self.base_url,
             timeout=self._resolved_api_call_timeout(),
             max_tokens=self.max_tokens,
             ephemeral_max_output_tokens=_ephemeral_out,
diff --git a/tests/run_agent/test_provider_parity.py b/tests/run_agent/test_provider_parity.py
index 5ad40e8a88..dabcb8b742 100644
--- a/tests/run_agent/test_provider_parity.py
+++ b/tests/run_agent/test_provider_parity.py
@@ -144,6 +144,36 @@ class TestBuildApiKwargsOpenRouter:
         assert messages[1]["tool_calls"][0]["response_item_id"] == "fc_123"
         assert "codex_reasoning_items" in messages[1]
 
+    def test_gemini_native_passes_base_url_for_top_level_thinking_config(self, monkeypatch):
+        agent = _make_agent(
+            monkeypatch,
+            "gemini",
+            base_url="https://generativelanguage.googleapis.com/v1beta",
+            model="gemini-3-flash-preview",
+        )
+        agent.reasoning_config = {"enabled": True, "effort": "high"}
+        kwargs = agent._build_api_kwargs([{"role": "user", "content": "hi"}])
+        assert kwargs["extra_body"]["thinking_config"] == {
+            "includeThoughts": True,
+            "thinkingLevel": "high",
+        }
+        assert "extra_body" not in kwargs["extra_body"]
+
+    def test_gemini_openai_compat_passes_base_url_for_nested_google_thinking_config(self, monkeypatch):
+        agent = _make_agent(
+            monkeypatch,
+            "gemini",
+            base_url="https://generativelanguage.googleapis.com/v1beta/openai",
+            model="gemini-3.1-pro-preview",
+        )
+        agent.reasoning_config = {"enabled": True, "effort": "high"}
+        kwargs = agent._build_api_kwargs([{"role": "user", "content": "hi"}])
+        assert "thinking_config" not in kwargs["extra_body"]
+        assert kwargs["extra_body"]["extra_body"]["google"]["thinking_config"] == {
+            "include_thoughts": True,
+            "thinking_level": "high",
+        }
+
     def test_should_sanitize_tool_calls_codex_vs_chat(self, monkeypatch):
         """Codex API should NOT sanitize, all other APIs should sanitize."""
         # Codex mode should NOT need sanitization