diff --git a/docs/api/changelog.rst b/docs/api/changelog.rst
index 82a3f5d96..acadd5334 100644
--- a/docs/api/changelog.rst
+++ b/docs/api/changelog.rst
@@ -9,6 +9,15 @@ The format is based on `Keep a Changelog`_, and this project adheres to
 [Unreleased]
 ------------
 
+Added
+~~~~~
+
+- Added ``ignore_time_purge_empty`` argument to
+  :meth:`imod.mf6.Modflow6Simulation.mask_all_models` and
+  :meth:`imod.mf6.Modflow6Simulation.clip_box` to consider a package empty if
+  its first times step is all nodata. This can save a lot of clipping or masking
+  transient models with many timesteps.
+
 Fixed
 ~~~~~
 
diff --git a/imod/common/utilities/mask.py b/imod/common/utilities/mask.py
index 7e0809145..b0199cb30 100644
--- a/imod/common/utilities/mask.py
+++ b/imod/common/utilities/mask.py
@@ -37,9 +37,10 @@ def _validate_coords_mask(mask: GridDataArray) -> None:
         )
 
 
-def _mask_all_models(
+def mask_all_models(
     simulation: ISimulation,
     mask: GridDataArray,
+    ignore_time_purge_empty: bool = False,
 ):
     _validate_coords_mask(mask)
     if simulation.is_split():
@@ -54,21 +55,22 @@ def _mask_all_models(
 
     for name in modelnames:
         if is_same_domain(simulation[name].domain, mask):
-            simulation[name].mask_all_packages(mask)
+            simulation[name].mask_all_packages(mask, ignore_time_purge_empty)
         else:
             raise ValueError(
                 "masking can only be applied to simulations when all the models in the simulation use the same grid."
             )
 
 
-def _mask_all_packages(
+def mask_all_packages(
     model: IModel,
     mask: GridDataArray,
+    ignore_time_purge_empty: bool = False,
 ):
     _validate_coords_mask(mask)
     for pkgname, pkg in model.items():
         model[pkgname] = pkg.mask(mask)
-    model.purge_empty_packages()
+    model.purge_empty_packages(ignore_time=ignore_time_purge_empty)
 
 
 def mask_package(package: IPackage, mask: GridDataArray) -> IPackage:
diff --git a/imod/mf6/model.py b/imod/mf6/model.py
index ee0de6da6..97c464be5 100644
--- a/imod/mf6/model.py
+++ b/imod/mf6/model.py
@@ -22,7 +22,7 @@
 from imod.common.serializer import EngineType
 from imod.common.statusinfo import NestedStatusInfo, StatusInfo, StatusInfoBase
 from imod.common.utilities.clip import clip_box_dataset
-from imod.common.utilities.mask import _mask_all_packages
+from imod.common.utilities.mask import mask_all_packages
 from imod.common.utilities.regrid import _regrid_like
 from imod.common.utilities.schemata import (
     concatenate_schemata_dicts,
@@ -697,6 +697,7 @@ def clip_box(
         y_min: Optional[float] = None,
         y_max: Optional[float] = None,
         state_for_boundary: Optional[GridDataArray] = None,
+        ignore_time_purge_empty: bool = False,
     ):
         """
         Clip a model by a bounding box (time, layer, y, x).
@@ -724,6 +725,14 @@ def clip_box(
         state_for_boundary : optional, Union[xr.DataArray, xu.UgridDataArray]
             A grids with states that are used to put as boundary values. This
             model will get a :class:`imod.mf6.ConstantHead`.
+        ignore_time_purge_empty : bool, default False
+            Whether to ignore the time dimension when purging empty packages.
+            Can improve performance when clipping models with many time steps.
+            Clipping models can cause package data with all nans. These packages
+            are considered empty and need to be removed. However, checking all
+            timesteps for each package is a costly operation. Therefore, this
+            option can be set to True to only check the first timestep. Defaults
+            to False.
 
         Returns
         -------
@@ -786,7 +795,7 @@ def clip_box(
         if clipped_boundary_condition is not None:
             clipped[pkg_name] = clipped_boundary_condition
 
-        clipped.purge_empty_packages()
+        clipped.purge_empty_packages(ignore_time=ignore_time_purge_empty)
 
         return clipped
 
@@ -882,6 +891,7 @@ def regrid_like(
     def mask_all_packages(
         self,
         mask: GridDataArray,
+        ignore_time_purge_empty: bool = False,
     ):
         """
         This function applies a mask to all packages in a model. The mask must
@@ -898,9 +908,12 @@ def mask_all_packages(
         mask: xr.DataArray, xu.UgridDataArray of ints
             idomain-like integer array. >0 sets cells to active, 0 sets cells to inactive,
             <0 sets cells to vertical passthrough
+        ignore_time_purge_empty: bool, default False
+            Whether to ignore time dimension when purging empty packages. Can
+            improve performance when masking models with many time steps.
         """
 
-        _mask_all_packages(self, mask)
+        mask_all_packages(self, mask, ignore_time_purge_empty)
 
     def purge_empty_packages(
         self, model_name: Optional[str] = "", ignore_time: bool = False
diff --git a/imod/mf6/simulation.py b/imod/mf6/simulation.py
index d3c734f5c..976219fbd 100644
--- a/imod/mf6/simulation.py
+++ b/imod/mf6/simulation.py
@@ -24,7 +24,7 @@
 from imod.common.serializer import EngineType
 from imod.common.statusinfo import NestedStatusInfo
 from imod.common.utilities.dataclass_type import DataclassType
-from imod.common.utilities.mask import _mask_all_models
+from imod.common.utilities.mask import mask_all_models
 from imod.common.utilities.regrid import _regrid_like
 from imod.common.utilities.version import (
     get_version,
@@ -1202,6 +1202,7 @@ def clip_box(
         y_min: Optional[float] = None,
         y_max: Optional[float] = None,
         states_for_boundary: Optional[dict[str, GridDataArray]] = None,
+        ignore_time_purge_empty: Optional[bool] = None,
     ) -> Modflow6Simulation:
         """
         Clip a simulation by a bounding box (time, layer, y, x).
@@ -1233,6 +1234,14 @@ def clip_box(
             :class:`imod.mf6.ConstantHead`,
             :class:`imod.mf6.GroundwaterTransportModel` will get a
             :class:`imod.mf6.ConstantConcentration` package.
+        ignore_time_purge_empty: optional, bool, default None
+            Whether to ignore the time dimension when purging empty packages.
+            Can improve performance when clipping models with many time steps.
+            Clipping models can cause package data with all nans. These packages
+            are considered empty and need to be removed. However, checking all
+            timesteps for each package is a costly operation. Therefore, this
+            option can be set to True to only check the first timestep. If None,
+            the value of the validation settings of the simulation are used.
 
         Returns
         -------
@@ -1276,6 +1285,8 @@ def clip_box(
             raise ValueError(
                 "Unable to clip simulation. Clipping can only be done on simulations that have a single flow model ."
             )
+        if ignore_time_purge_empty is None:
+            ignore_time_purge_empty = self._validation_context.ignore_time
         for model_name, model in self.get_models().items():
             supported, error_with_object = model._is_clipping_supported()
             if not supported:
@@ -1301,6 +1312,7 @@ def clip_box(
                     y_min=y_min,
                     y_max=y_max,
                     state_for_boundary=state_for_boundary,
+                    ignore_time_purge_empty=ignore_time_purge_empty,
                 )
             elif isinstance(value, Package):
                 clipped[key] = value.clip_box(
@@ -1398,11 +1410,14 @@ def split(
             similar shape as a layer in the domain. The values in the array
             indicate to which partition a cell belongs. The values should be
             zero or greater.
-        ignore_time_purge_empty: bool, default None
-            If True, only the first timestep is validated. This increases
-            performance for packages with a time dimensions over which changes
-            of cell activity are not expected. If None, the value of the
-            validation context is of the simulation is used.
+        ignore_time_purge_empty: optional, bool, default None
+            Whether to ignore the time dimension when purging empty packages.
+            Can improve performance when splitting models with many time steps.
+            Splitting models can cause package data with all nans. These packages
+            are considered empty and need to be removed. However, checking all
+            timesteps for each package is a costly operation. Therefore, this
+            option can be set to True to only check the first timestep. If None,
+            the value of the validation settings of the simulation are used.
 
         Returns
         -------
@@ -1688,6 +1703,7 @@ def _has_one_flow_model(self) -> bool:
     def mask_all_models(
         self,
         mask: GridDataArray,
+        ignore_time_purge_empty: Optional[bool] = None,
     ) -> None:
         """
         This function applies a mask to all models in a simulation, provided they use
@@ -1702,6 +1718,14 @@ def mask_all_models(
         mask: xr.DataArray, xu.UgridDataArray of ints
             idomain-like integer array. >0 sets cells to active, 0 sets cells to inactive,
             <0 sets cells to vertical passthrough
+        ignore_time_purge_empty : bool, default False
+            Whether to ignore the time dimension when purging empty packages.
+            Can improve performance when masking models with many time steps.
+            Masking models can cause package data with all nans. These packages
+            are considered empty and need to be removed. However, checking all
+            timesteps for each package is a costly operation. Therefore, this
+            option can be set to True to only check the first timestep. Defaults
+            to False.
 
         Examples
         --------
@@ -1713,7 +1737,9 @@ def mask_all_models(
         mask should be an idomain-like array, i.e. it should have the same shape
         as the model and contain integer values.
         """
-        _mask_all_models(self, mask)
+        if ignore_time_purge_empty is None:
+            ignore_time_purge_empty = self._validation_context.ignore_time
+        mask_all_models(self, mask, ignore_time_purge_empty)
 
     @classmethod
     @standard_log_decorator()
diff --git a/imod/tests/test_mf6/test_mf6_LHM.py b/imod/tests/test_mf6/test_mf6_LHM.py
index 44a8812c9..6fa13a852 100644
--- a/imod/tests/test_mf6/test_mf6_LHM.py
+++ b/imod/tests/test_mf6/test_mf6_LHM.py
@@ -78,7 +78,7 @@ def cleanup_mf6_sim(simulation: Modflow6Simulation) -> None:
         pkg.dataset.load()
 
     mask = model.domain
-    simulation.mask_all_models(mask)
+    simulation.mask_all_models(mask, ignore_time_purge_empty=True)
     dis = model["dis"]
 
     pkgs_to_cleanup = [
diff --git a/imod/tests/test_mf6/test_mf6_mask_simulation.py b/imod/tests/test_mf6/test_mf6_mask_simulation.py
index 575693503..6058a49b1 100644
--- a/imod/tests/test_mf6/test_mf6_mask_simulation.py
+++ b/imod/tests/test_mf6/test_mf6_mask_simulation.py
@@ -9,13 +9,15 @@
 from imod.tests.fixtures.mf6_modelrun_fixture import assert_simulation_can_run
 
 
+@pytest.mark.parametrize("ignore_time", [True, False])
 def test_mask_simulation(
     tmp_path: Path,
     flow_transport_simulation: imod.mf6.Modflow6Simulation,
+    ignore_time: bool,
 ):
     mask = deepcopy(flow_transport_simulation["flow"].domain)
     mask.loc[1, 0.5, 15] = 0
-    flow_transport_simulation.mask_all_models(mask)
+    flow_transport_simulation.mask_all_models(mask, ignore_time_purge_empty=ignore_time)
     assert (
         flow_transport_simulation["flow"].domain.sel({"layer": 1, "y": 0.5, "x": 15})
         == 0
diff --git a/imod/tests/test_mf6/test_mf6_model_masking.py b/imod/tests/test_mf6/test_mf6_model_masking.py
index ed8bbb71a..94355e352 100644
--- a/imod/tests/test_mf6/test_mf6_model_masking.py
+++ b/imod/tests/test_mf6/test_mf6_model_masking.py
@@ -266,11 +266,13 @@ def test_mask_with_time_coordinate(
 @pytest.mark.parametrize(
     "inactivity_marker", [0, -1]
 )  # 0 = inactive, -1 = vertical passthrough
+@pytest.mark.parametrize("ignore_time_purge_empty", [True, False])
 def test_mask_structured(
     tmp_path: Path,
     structured_flow_model: GroundwaterFlowModel,
     mask_cells: list[tuple[int, int, int]],
     inactivity_marker: int,
+    ignore_time_purge_empty: bool,
 ):
     # Arrange
     # add a well to the model
@@ -291,7 +293,9 @@ def test_mask_structured(
         mask.values[*cell] = inactivity_marker
 
     # Act
-    structured_flow_model.mask_all_packages(mask)
+    structured_flow_model.mask_all_packages(
+        mask, ignore_time_purge_empty=ignore_time_purge_empty
+    )
 
     # Assert
     unique, counts = np.unique(
diff --git a/imod/tests/test_mf6/test_mf6_rch.py b/imod/tests/test_mf6/test_mf6_rch.py
index b8b11f64e..ae8c8037f 100644
--- a/imod/tests/test_mf6/test_mf6_rch.py
+++ b/imod/tests/test_mf6/test_mf6_rch.py
@@ -297,8 +297,16 @@ def test_validate_false():
 
 @pytest.mark.timeout(10, method="thread")
 def test_ignore_time_validation():
-    # Create a large recharge dataset with a time dimension. This is to test the
-    # performance of the validation when ignore_time_no_data is True.
+    """
+    Create a large recharge dataset with a time dimension. This is to test the
+    performance of the validation when ignore_time_no_data is True.
+    NOTE: There currently is no easy way to test the opposite (i.e.,
+    ignore_time_no_data is False, then catch timeout with an pytest xfail
+    marker), because the timeout will terminate the test run with an error when
+    using dask instead of a fail. Somewhat relevant issue:
+    https://github.com/pytest-dev/pytest-timeout/issues/181
+    """
+    # Arrange
     rng = dask.array.random.default_rng()
     layer = [1, 2, 3]
     template = imod.util.empty_3d(1.0, 0.0, 1000.0, 1.0, 0.0, 1000.0, layer)
diff --git a/imod/tests/test_mf6/test_mf6_simulation.py b/imod/tests/test_mf6/test_mf6_simulation.py
index 81b9e827c..06a9be30c 100644
--- a/imod/tests/test_mf6/test_mf6_simulation.py
+++ b/imod/tests/test_mf6/test_mf6_simulation.py
@@ -278,6 +278,14 @@ def test_write_circle_model_twice(circle_model, tmp_path):
     assert len(diff.right_only) == 0
 
 
+@pytest.mark.parametrize("ignore_time_purge_empty", [True, False])
+def test_simulation_clip_box__ignore_time(circle_model, ignore_time_purge_empty):
+    simulation = circle_model
+    simulation.clip_box(
+        y_min=-50, y_max=0, ignore_time_purge_empty=ignore_time_purge_empty
+    )
+
+
 def test_simulation_clip_box__validation_settings_preserved(circle_model):
     simulation = circle_model
     simulation.set_validation_settings(