diff --git a/jax/_src/cloud_tpu_init.py b/jax/_src/cloud_tpu_init.py
index 82219886b..0539e4253 100644
--- a/jax/_src/cloud_tpu_init.py
+++ b/jax/_src/cloud_tpu_init.py
@@ -15,6 +15,7 @@
 import datetime
 import os
 import re
+import warnings
 from jax import version
 from jax._src import config
 from jax._src import hardware_utils
@@ -72,7 +73,19 @@ def cloud_tpu_init() -> None:
 
   # Exit early if we're not running on a Cloud TPU VM or libtpu isn't installed.
   libtpu_path = get_tpu_library_path()
-  num_tpu_chips = hardware_utils.num_available_tpu_chips_and_device_id()[0]
+  num_tpu_chips, tpu_id = hardware_utils.num_available_tpu_chips_and_device_id()
+  if (
+      tpu_id is not None
+      and tpu_id >= hardware_utils.TpuVersion.v5e
+      and not hardware_utils.transparent_hugepages_enabled()
+  ):
+    warnings.warn(
+        'Transparent hugepages are not enabled. TPU runtime startup and'
+        ' shutdown time should be significantly improved on TPU v5e and newer.'
+        ' If not already set, you may need to enable transparent hugepages in'
+        ' your VM image (sudo sh -c "echo always >'
+        ' /sys/kernel/mm/transparent_hugepage/enabled")'
+    )
   if (libtpu_path is None or num_tpu_chips == 0) and not jax_force_tpu_init():
     return
 
diff --git a/jax/_src/hardware_utils.py b/jax/_src/hardware_utils.py
index 81ef07a71..84ad9edf9 100644
--- a/jax/_src/hardware_utils.py
+++ b/jax/_src/hardware_utils.py
@@ -12,25 +12,12 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import enum
 import os
 import pathlib
 import glob
 
 _GOOGLE_PCI_VENDOR_ID = '0x1ae0'
-_TPU_PCI_DEVICE_IDS = [
-    # TPU v2, v3
-    '0x0027',
-    # No public name (plc)
-    '0x0056',
-    # TPU v4
-    '0x005e',
-    # TPU v5p
-    '0x0062',
-    # TPU v5e
-    '0x0063',
-    # TPU v6e
-    '0x006f',
-]
 
 _NVIDIA_GPU_DEVICES = [
     '/dev/nvidia0',
@@ -38,10 +25,36 @@ _NVIDIA_GPU_DEVICES = [
     '/dev/dxg',  # WSL2
 ]
 
+
+class TpuVersion(enum.IntEnum):
+  # TPU v2, v3
+  v2 = 0
+  v3 = 1
+  # No public name (plc)
+  plc = 2
+  # TPU v4
+  v4 = 3
+  # TPU v5p
+  v5p = 4
+  # TPU v5e
+  v5e = 5
+  # TPU v6e
+  v6e = 6
+
+
+_TPU_PCI_DEVICE_IDS = {
+    '0x0027': TpuVersion.v3,
+    '0x0056': TpuVersion.plc,
+    '0x005e': TpuVersion.v4,
+    '0x0062': TpuVersion.v5p,
+    '0x0063': TpuVersion.v5e,
+    '0x006f': TpuVersion.v6e,
+}
+
 def num_available_tpu_chips_and_device_id():
   """Returns the device id and number of TPU chips attached through PCI."""
   num_chips = 0
-  device_id = ''
+  tpu_version = None
   for vendor_path in glob.glob('/sys/bus/pci/devices/*/vendor'):
     vendor_id = pathlib.Path(vendor_path).read_text().strip()
     if vendor_id != _GOOGLE_PCI_VENDOR_ID:
@@ -50,12 +63,20 @@ def num_available_tpu_chips_and_device_id():
     device_path = os.path.join(os.path.dirname(vendor_path), 'device')
     device_id = pathlib.Path(device_path).read_text().strip()
     if device_id in _TPU_PCI_DEVICE_IDS:
+      tpu_version = _TPU_PCI_DEVICE_IDS[device_id]
       num_chips += 1
 
-  return num_chips, device_id
+  return num_chips, tpu_version
 
 
 def has_visible_nvidia_gpu() -> bool:
   """True if there's a visible nvidia gpu available on device, False otherwise."""
 
   return any(os.path.exists(d) for d in _NVIDIA_GPU_DEVICES)
+
+
+def transparent_hugepages_enabled() -> bool:
+  # See https://docs.kernel.org/admin-guide/mm/transhuge.html for more
+  # information about transparent huge pages.
+  path = pathlib.Path('/sys/kernel/mm/transparent_hugepage/enabled')
+  return path.exists() and path.read_text().strip() == '[always] madvise never'
diff --git a/pyproject.toml b/pyproject.toml
index e32b14a89..a1b9e7dd4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,6 +66,9 @@ filterwarnings = [
     # https://github.com/protocolbuffers/protobuf/issues/12186#issuecomment-1745679358
     "ignore:Type google\\._upb\\._message\\.(Scalar|Message)MapContainer uses PyType_Spec with a metaclass that has custom tp_new\\. This is deprecated and will no longer be allowed in Python 3\\.14\\.:DeprecationWarning",
 
+    # TODO(b/401588349): Remove this once transparent hugepages are enabled.
+    "ignore:Transparent hugepages",
+
     # NOTE: this is probably not where you want to add code to suppress a
     # warning. Only pytest tests look at this list, whereas Bazel tests also
     # check for warnings and do not check this list. Most likely, you should