diff --git a/docs/api/changelog.rst b/docs/api/changelog.rst
index 9942338e7..de7d1156c 100644
--- a/docs/api/changelog.rst
+++ b/docs/api/changelog.rst
@@ -56,6 +56,8 @@ Fixed
   a layer in the model discretization, which would cause these cells to be
   dropped when distributing conductances later.
 - Fixed :func:`imod.prepare.spatial.polygonize` for polygons with holes.
+- :func:`imod.formats.prj.open_projectfile_data` now drops empty wells from the
+  dataset, and logs a warning about it.
 
 Changed
 ~~~~~~~
diff --git a/imod/formats/prj/prj.py b/imod/formats/prj/prj.py
index da51a90cb..8bb1e1887 100644
--- a/imod/formats/prj/prj.py
+++ b/imod/formats/prj/prj.py
@@ -915,6 +915,15 @@ def _read_package_ipf(
         # Ensure the columns are identifiable.
         path = Path(entry["path"])
         ipf_df, indexcol, ext = _try_read_with_func(imod.ipf._read_ipf, path)
+        nrow = ipf_df.shape[0]
+        if nrow == 0:
+            log_message = f"IPF file {path} contains no data. Skipping."
+            imod.logging.logger.log(
+                loglevel=LogLevel.WARNING,
+                message=log_message,
+                additional_depth=0,
+            )
+            continue
         if indexcol == 0:
             # No associated files
             has_associated = False
diff --git a/imod/tests/conftest.py b/imod/tests/conftest.py
index 0670d85d0..9bc606476 100644
--- a/imod/tests/conftest.py
+++ b/imod/tests/conftest.py
@@ -29,6 +29,7 @@
 )
 from .fixtures.imod5_well_data import (
     well_duplication_import_prj,
+    well_empty_ipfs,
     well_mixed_ipfs,
     well_out_of_bounds_ipfs,
     well_regular_import_prj,
diff --git a/imod/tests/fixtures/imod5_well_data.py b/imod/tests/fixtures/imod5_well_data.py
index 4ca196614..a3e24de47 100644
--- a/imod/tests/fixtures/imod5_well_data.py
+++ b/imod/tests/fixtures/imod5_well_data.py
@@ -188,6 +188,36 @@ def out_of_bounds_timeseries_string():
     )
 
 
+def ipf_simple_empty():
+    """
+    Empty ipf file with only the header and zero rows. iMOD5 can generate these
+    files after clipping an existing database.
+    """
+    ipf_simple_header_copy = "0" + ipf_simple_header[ipf_simple_header.find("\n") :]
+
+    return textwrap.dedent(
+        f"""\
+    {ipf_simple_header_copy}
+    """
+    )
+
+
+def ipf_associated_empty():
+    """
+    Empty associated ipf file with only the header and zero rows. iMOD5 can generate these
+    files after clipping an existing database.
+    """
+    ipf_associated_header_copy = (
+        "0" + ipf_associated_header[ipf_associated_header.find("\n") :]
+    )
+
+    return textwrap.dedent(
+        f"""\
+    {ipf_associated_header_copy}
+    """
+    )
+
+
 def write_ipf_and_maybe_assoc_files(
     tmp_path,
     projectfile_str,
@@ -337,3 +367,14 @@ def well_out_of_bounds_ipfs():
         other_timeseries_well_str,
         tmp_path,
     )
+
+
+@pytest.fixture(scope="session")
+def well_empty_ipfs():
+    tmp_path = imod.util.temporary_directory()
+    os.makedirs(tmp_path)
+
+    ipf1_str = ipf_simple_empty()
+    ipf_associated_str = ipf_associated_empty()
+
+    return write_ipf_mixed_files(ipf_associated_str, ipf1_str, "", "", tmp_path)
diff --git a/imod/tests/test_formats/test_prj_wel.py b/imod/tests/test_formats/test_prj_wel.py
index e5e535743..ef90b7582 100644
--- a/imod/tests/test_formats/test_prj_wel.py
+++ b/imod/tests/test_formats/test_prj_wel.py
@@ -1,3 +1,4 @@
+import sys
 from datetime import datetime
 from shutil import copyfile
 from textwrap import dedent
@@ -13,7 +14,8 @@
     parametrize_with_cases,
 )
 
-from imod.formats.prj import open_projectfile_data
+from imod.formats.prj import open_projectfile_data, read_projectfile
+from imod.logging import LoggerType, LogLevel, configure
 from imod.mf6 import LayeredWell, Well
 
 
@@ -946,3 +948,47 @@ def test_from_imod5_data_wells__wells_out_of_bounds(
                 expected_last_rate = data[wellname]["dataframe"][0]["rate"].iloc[-2]
                 actual_last_rate = well.dataset["rate"].isel(index=1, time=-1).item()
                 assert actual_last_rate == expected_last_rate
+
+
+@pytest.mark.unittest_jit
+@parametrize("wel_case", argvalues=PRJ_ARGS)
+@parametrize("wel_cls", argvalues=[LayeredWell, Well])
+def test_from_imod5_data_wells__empty_wells(
+    wel_cls: Union[LayeredWell, Well],
+    wel_case,
+    well_empty_ipfs,
+    tmp_path,
+    request,
+):
+    # Arrange
+    # Replace layer number to zero if non-layered well.
+    if wel_cls == Well:
+        wel_case = wel_case.replace("1,2, 001", "1,2, 000")
+    # Write prj and copy ipfs to right folder.
+    case_name = get_case_name(request)
+    wel_file = tmp_path / f"{case_name}.prj"
+    setup_test_files(wel_case, wel_file, well_empty_ipfs, tmp_path)
+
+    projectfile_contents = read_projectfile(wel_file)
+
+    # Act
+    logfile_path = tmp_path / "logfile.txt"
+    with open(logfile_path, "w") as sys.stdout:
+        configure(
+            LoggerType.LOGURU,
+            log_level=LogLevel.WARNING,
+            add_default_file_handler=False,
+            add_default_stream_handler=True,
+        )
+        data, _ = open_projectfile_data(wel_file)
+
+    with open(logfile_path, "r") as f:
+        log = f.read()
+
+    # Assert
+    # Projectfile only contains empty wells, so expect empty data.
+    assert len(data) == 0
+    # Expect warning about empty wells.
+    for ipf_contents in projectfile_contents["(wel)"]["ipf"]:
+        ipf_path = ipf_contents["path"]
+        assert f"IPF file {ipf_path} contains no data. Skipping." in log