diff --git a/mypy/cache.py b/mypy/cache.py
index 832cfb4732ea..f67bd627d3b8 100644
--- a/mypy/cache.py
+++ b/mypy/cache.py
@@ -1,7 +1,7 @@
 """
 This module contains high-level logic for fixed format serialization.
 
-Lower-level parts are implemented in C in mypyc/lib-rt/librt_internal.c
+Lower-level parts are implemented in C in mypyc/lib-rt/internal/librt_internal.c
 Short summary of low-level functionality:
 * integers are automatically serialized as 1, 2, or 4 bytes, or arbitrary length.
 * str/bytes are serialized as size (1, 2, or 4 bytes) followed by bytes buffer.
diff --git a/mypyc/build.py b/mypyc/build.py
index ef5d00fca145..08c08685ea1e 100644
--- a/mypyc/build.py
+++ b/mypyc/build.py
@@ -53,12 +53,12 @@ class ModDesc(NamedTuple):
 
 
 LIBRT_MODULES = [
-    ModDesc("librt.internal", ["librt_internal.c"], [], []),
-    ModDesc("librt.strings", ["librt_strings.c"], [], []),
+    ModDesc("librt.internal", ["internal/librt_internal.c"], [], ["internal"]),
+    ModDesc("librt.strings", ["strings/librt_strings.c"], [], ["strings"]),
     ModDesc(
         "librt.base64",
         [
-            "librt_base64.c",
+            "base64/librt_base64.c",
             "base64/lib.c",
             "base64/codec_choose.c",
             "base64/tables/tables.c",
diff --git a/mypyc/codegen/emitmodule.py b/mypyc/codegen/emitmodule.py
index a345753a74dd..d56dfd766e1c 100644
--- a/mypyc/codegen/emitmodule.py
+++ b/mypyc/codegen/emitmodule.py
@@ -625,11 +625,11 @@ def generate_c_for_modules(self) -> list[tuple[str, str]]:
         ext_declarations.emit_line("#include <Python.h>")
         ext_declarations.emit_line("#include <CPy.h>")
         if self.compiler_options.depends_on_librt_internal:
-            ext_declarations.emit_line("#include <librt_internal.h>")
+            ext_declarations.emit_line("#include <internal/librt_internal.h>")
         if any(LIBRT_BASE64 in mod.dependencies for mod in self.modules.values()):
-            ext_declarations.emit_line("#include <librt_base64.h>")
+            ext_declarations.emit_line("#include <base64/librt_base64.h>")
         if any(LIBRT_STRINGS in mod.dependencies for mod in self.modules.values()):
-            ext_declarations.emit_line("#include <librt_strings.h>")
+            ext_declarations.emit_line("#include <strings/librt_strings.h>")
         # Include headers for conditional source files
         source_deps = collect_source_dependencies(self.modules)
         for source_dep in sorted(source_deps, key=lambda d: d.path):
diff --git a/mypyc/lib-rt/librt_base64.c b/mypyc/lib-rt/base64/librt_base64.c
similarity index 100%
rename from mypyc/lib-rt/librt_base64.c
rename to mypyc/lib-rt/base64/librt_base64.c
diff --git a/mypyc/lib-rt/librt_base64.h b/mypyc/lib-rt/base64/librt_base64.h
similarity index 100%
rename from mypyc/lib-rt/librt_base64.h
rename to mypyc/lib-rt/base64/librt_base64.h
diff --git a/mypyc/lib-rt/byteswriter_extra_ops.h b/mypyc/lib-rt/byteswriter_extra_ops.h
index 59410a077fcd..27645052c782 100644
--- a/mypyc/lib-rt/byteswriter_extra_ops.h
+++ b/mypyc/lib-rt/byteswriter_extra_ops.h
@@ -6,7 +6,7 @@
 #include <stdint.h>
 #include <Python.h>
 
-#include "librt_strings.h"
+#include "strings/librt_strings.h"
 
 static inline CPyTagged
 CPyBytesWriter_Len(PyObject *obj) {
diff --git a/mypyc/lib-rt/librt_internal.c b/mypyc/lib-rt/internal/librt_internal.c
similarity index 100%
rename from mypyc/lib-rt/librt_internal.c
rename to mypyc/lib-rt/internal/librt_internal.c
diff --git a/mypyc/lib-rt/librt_internal.h b/mypyc/lib-rt/internal/librt_internal.h
similarity index 100%
rename from mypyc/lib-rt/librt_internal.h
rename to mypyc/lib-rt/internal/librt_internal.h
diff --git a/mypyc/lib-rt/setup.py b/mypyc/lib-rt/setup.py
index 964b56e4b562..a86e2367c1c0 100644
--- a/mypyc/lib-rt/setup.py
+++ b/mypyc/lib-rt/setup.py
@@ -89,33 +89,33 @@ def run(self) -> None:
             Extension(
                 "librt.internal",
                 [
-                    "librt_internal.c",
+                    "internal/librt_internal.c",
                     "init.c",
                     "int_ops.c",
                     "exc_ops.c",
                     "pythonsupport.c",
                     "getargsfast.c",
                 ],
-                include_dirs=["."],
+                include_dirs=[".", "internal"],
                 extra_compile_args=cflags,
             ),
             Extension(
                 "librt.strings",
                 [
-                    "librt_strings.c",
+                    "strings/librt_strings.c",
                     "init.c",
                     "int_ops.c",
                     "exc_ops.c",
                     "pythonsupport.c",
                     "getargsfast.c",
                 ],
-                include_dirs=["."],
+                include_dirs=[".", "strings"],
                 extra_compile_args=cflags,
             ),
             Extension(
                 "librt.base64",
                 [
-                    "librt_base64.c",
+                    "base64/librt_base64.c",
                     "base64/lib.c",
                     "base64/codec_choose.c",
                     "base64/tables/tables.c",
diff --git a/mypyc/lib-rt/librt_strings.c b/mypyc/lib-rt/strings/librt_strings.c
similarity index 100%
rename from mypyc/lib-rt/librt_strings.c
rename to mypyc/lib-rt/strings/librt_strings.c
diff --git a/mypyc/lib-rt/librt_strings.h b/mypyc/lib-rt/strings/librt_strings.h
similarity index 100%
rename from mypyc/lib-rt/librt_strings.h
rename to mypyc/lib-rt/strings/librt_strings.h
diff --git a/mypyc/lib-rt/stringwriter_extra_ops.h b/mypyc/lib-rt/stringwriter_extra_ops.h
index 646199c697f6..e15eb1dd2156 100644
--- a/mypyc/lib-rt/stringwriter_extra_ops.h
+++ b/mypyc/lib-rt/stringwriter_extra_ops.h
@@ -6,7 +6,7 @@
 #include <stdint.h>
 #include <Python.h>
 
-#include "librt_strings.h"
+#include "strings/librt_strings.h"
 
 static inline CPyTagged
 CPyStringWriter_Len(PyObject *obj) {