diff --git a/.gitmodules b/.gitmodules
index 58e22edefcec..2c6c117e9c57 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -7,10 +7,6 @@
 [submodule "third_party/vulkan_headers"]
 	path = third_party/vulkan_headers
 	url = https://github.com/KhronosGroup/Vulkan-Headers.git
-[submodule "third_party/pybind11"]
-	path = third_party/pybind11
-	url = https://github.com/pybind/pybind11.git
-	branch = stable
 [submodule "third_party/benchmark"]
 	path = third_party/benchmark
 	url = https://github.com/google/benchmark.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3e34ee8b05bd..a8a9b70bfa44 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -772,6 +772,30 @@ endif()
 # MLIR/LLVM Dependency
 #-------------------------------------------------------------------------------
 
+# Both the IREE and MLIR Python bindings require pybind11. We initialize it here
+# at the top level so that everything uses ours consistently.
+if(IREE_BUILD_PYTHON_BINDINGS AND IREE_BUILD_COMPILER)
+  set(pybind11_VERSION 2.13.6)
+  include(FetchContent)
+  FetchContent_Declare(
+      pybind11
+      GIT_REPOSITORY https://github.com/pybind/pybind11
+      GIT_TAG        v${pybind11_VERSION}
+  )
+  set(PYBIND11_FINDPYTHON ON)
+  FetchContent_MakeAvailable(pybind11)
+  # pybind11 source fetches do not include find_package integration, which is
+  # a shame since sub-projects can require that to work. If we were using
+  # CMake 3.24, we could just add OVERRIDE_FIND_PACKAGE to the
+  # FetchContent_Declare call above and it would take care of doing the
+  # following to let subsequent sub-project find_package calls to resolve
+  # successfully.
+  set(pybind11_DIR "${pybind11_BINARY_DIR}")
+  file(WRITE "${pybind11_BINARY_DIR}/pybind11Config.cmake" "")
+  file(WRITE "${pybind11_BINARY_DIR}/pybind11ConfigVersion.cmake"
+       "set(PACKAGE_VERSION ${pybind11_VERSION})\nset(PACKAGE_VERSION_COMPATIBLE TRUE)")
+endif()
+
 if(NOT IREE_BUILD_COMPILER)
   message(STATUS "Not adding LLVM/MLIR because the configuration does not require it")
 else()
@@ -921,19 +945,6 @@ if(IREE_BUILD_TESTS)
   include(iree_configure_testing)
 endif()
 
-if(IREE_BUILD_PYTHON_BINDINGS)
-  # The compiler uses pybind11
-  if(IREE_BUILD_COMPILER)
-    if(NOT TARGET pybind11::module)
-      message(STATUS "Using bundled pybind11")
-      set(PYBIND11_FINDPYTHON ON)
-      add_subdirectory(third_party/pybind11 EXCLUDE_FROM_ALL)
-    else()
-      message(STATUS "Not including bundled pybind11 (already configured)")
-    endif()
-  endif()
-endif()
-
 if(IREE_TARGET_BACKEND_METAL_SPIRV)
   # SPIRV-Cross is needed to cross compile SPIR-V into MSL source code.
   iree_set_spirv_cross_cmake_options()
diff --git a/compiler/pyproject.toml b/compiler/pyproject.toml
index 5a07bd90cc5e..b7a4fd4de382 100644
--- a/compiler/pyproject.toml
+++ b/compiler/pyproject.toml
@@ -3,15 +3,10 @@ requires = [
     "setuptools>=42",
     "wheel",
     "cmake",
-    # Note that the compiler wheel does not presently need nanobind, but
-    # it's build is enabled by the same flag which enables the runtime
-    # configuration, which does.
-    "nanobind==2.2.0",
     "ninja",
     # MLIR build depends.
     "numpy",
     "packaging",
-    "pybind11==2.13.6",
     "sympy",
 ]
 build-backend = "setuptools.build_meta"
diff --git a/runtime/bindings/python/CMakeLists.txt b/runtime/bindings/python/CMakeLists.txt
index 5ba7b84fbcf9..35a85d190a27 100644
--- a/runtime/bindings/python/CMakeLists.txt
+++ b/runtime/bindings/python/CMakeLists.txt
@@ -4,21 +4,14 @@
 # See https://llvm.org/LICENSE.txt for license information.
 # SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
 
-if(NOT nanobind_FOUND)
-  find_package(nanobind CONFIG QUIET)
-  if(NOT nanobind_FOUND)
-    execute_process(
-      COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
-      OUTPUT_STRIP_TRAILING_WHITESPACE
-      OUTPUT_VARIABLE NB_DIR
-      RESULT_VARIABLE RC)
-    if(RC AND NOT RC EQUAL 0)
-      message(WARNING "Probing for nanobind failed. Please install the project's Python dependencies or '${Python_EXECUTABLE} -m pip install nanobind'")
-    endif()
-    list(APPEND CMAKE_PREFIX_PATH "${NB_DIR}")
-  endif()
-  find_package(nanobind CONFIG REQUIRED)
-endif()
+# nanobind
+include(FetchContent)
+FetchContent_Declare(
+  nanobind
+  GIT_REPOSITORY https://github.com/wjakob/nanobind.git
+  GIT_TAG        784efa2a0358a4dc5432c74f5685ee026e20f2b6 # 2.2.0
+)
+FetchContent_MakeAvailable(nanobind)
 
 set(_EXTRA_INSTALL_TOOL_TARGETS)
 set(_TRACY_ENABLED OFF)
diff --git a/runtime/bindings/python/iree/runtime/build_requirements.txt b/runtime/bindings/python/iree/runtime/build_requirements.txt
index e3f07b20f0bb..0a8dca312c7d 100644
--- a/runtime/bindings/python/iree/runtime/build_requirements.txt
+++ b/runtime/bindings/python/iree/runtime/build_requirements.txt
@@ -5,12 +5,7 @@
 
 pip>=21.3
 setuptools>=62.4.0
-nanobind==2.2.0
 numpy>=2.0.0b1
 requests>=2.28.0
 wheel>=0.36.2
 sympy==1.12.1
-
-# TODO: nanobind is used in the runtime but the compiler uses pybind and
-# removing this breaks CI bots; remove this.
-pybind11==2.13.6
diff --git a/runtime/pyproject.toml b/runtime/pyproject.toml
index 3259f736c8db..16567a601072 100644
--- a/runtime/pyproject.toml
+++ b/runtime/pyproject.toml
@@ -3,7 +3,6 @@ requires = [
     "setuptools>=42",
     "wheel",
     "cmake",
-    "nanobind==2.2.0",
     "ninja",
     "numpy>=2.0.0b1",
     "packaging",
diff --git a/third_party/pybind11 b/third_party/pybind11
deleted file mode 160000
index a2e59f0e7065..000000000000
--- a/third_party/pybind11
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit a2e59f0e7065404b44dfe92a28aca47ba1378dc4