diff --git a/src/runtime/jsc_hooks.rs b/src/runtime/jsc_hooks.rs
index 3c20e0cea402..bfc6e9d89311 100644
--- a/src/runtime/jsc_hooks.rs
+++ b/src/runtime/jsc_hooks.rs
@@ -2652,6 +2652,18 @@ fn transpile_source_code_inner(
                     return Err(crate::Error::ParseError);
                 }
 
+                // Mark the entry point as loaded as soon as it has parsed
+                // successfully, before any of the early `Ok(...)` returns below
+                // (bytecode, empty-cjs, runtime-transpiler-cache hit, etc.).
+                // `has_loaded` is what flips the loader fallback for unknown
+                // extensions (`transpile_file`'s `synchronous_loader` block) from
+                // `Tsx` to `File`; leaving it unset on a cache hit made a second
+                // run of `bun entry.ts` parse `import x from "./a.c"` as JS.
+                if is_main {
+                    // SAFETY: per fn contract — `jsc_vm` is the live per-thread VM.
+                    unsafe { (*jsc_vm).has_loaded = true };
+                }
+
                 let source = &parse_result.source;
 
                 // Raw JSON: hand the source bytes straight to JSC.
@@ -3050,11 +3062,6 @@ fn transpile_source_code_inner(
                     print_result?;
                 }
 
-                if is_main {
-                    // SAFETY: per fn contract — `jsc_vm` is the live per-thread VM.
-                    unsafe { (*jsc_vm).has_loaded = true };
-                }
-
                 // `module_info.asDeserialized()`: finalize the
                 // printer-filled record into the FFI shape consumed by C++
                 // (freed by C++ `~SourceProvider` via
diff --git a/test/cli/run/transpiler-cache.test.ts b/test/cli/run/transpiler-cache.test.ts
index d9a09d5163d1..a2b4f3c184d4 100644
--- a/test/cli/run/transpiler-cache.test.ts
+++ b/test/cli/run/transpiler-cache.test.ts
@@ -223,6 +223,42 @@ describe("transpiler cache", () => {
     expect(b.stdout == "production 5");
     expect(newCacheCount()).toBe(0);
   });
+  test("cache hit on the entry point does not change loader selection for unknown-extension imports", () => {
+    // The runtime-transpiler-cache early return used to skip marking the VM's
+    // `has_loaded` flag, so on a warm run (>= MINIMUM_CACHE_SIZE entry file
+    // served from cache) an ESM `import x from "./file.c"` fell into the
+    // "potentially the main module" loader fallback and tried to parse the
+    // C source as TSX instead of using the file loader.
+    writeFileSync(join(temp_dir, "impl.c"), "#include <stdio.h>\nint main() { return 0; }\n");
+    // Entry file large enough to be cached, importing an unknown-extension file.
+    const code =
+      'import src from "./impl.c";\nconsole.log(typeof src === "string" && src.endsWith("impl.c") ? "file-loader-ok" : src);\n';
+    writeFileSync(join(temp_dir, "entry.ts"), code + "//" + Buffer.alloc(50 * 1024, "x").toString() + "\n");
+
+    const run = (label: string) => {
+      const result = Bun.spawnSync({
+        cmd: [bunExe(), "entry.ts"],
+        cwd: temp_dir,
+        env,
+      });
+      const stderr = result.stderr.toString();
+      const stdout = result.stdout.toString().trim();
+      if (!result.success) throw new Error(`${label}: ${stderr}\n${stdout}`);
+      return { stdout, stderr };
+    };
+
+    const cold = run("cold run");
+    expect(cold.stdout).toBe("file-loader-ok");
+    expect(existsSync(cache_dir)).toBeTrue();
+    expect(newCacheCount()).toBe(1);
+
+    // On the warm run the entry point is restored from cache; the `.c` import
+    // must still go through the file loader.
+    const warm = run("warm run (cache hit)");
+    expect(warm.stderr).not.toContain("Unexpected #include");
+    expect(warm.stdout).toBe("file-loader-ok");
+    expect(newCacheCount()).toBe(0);
+  });
   test("--feature flag invalidates cache", () => {
     // feature() can only appear in an if/ternary, so wrap it
     const code = `import { feature } from "bun:bundle";\nif (feature("SUPER_SECRET")) console.log("enabled"); else console.log("disabled");`;