diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
index b8d611ba0c8..3629f14cd69 100644
--- a/pygmt/clib/session.py
+++ b/pygmt/clib/session.py
@@ -27,7 +27,6 @@
 from pygmt.exceptions import (
     GMTCLibError,
     GMTCLibNoSessionError,
-    GMTInvalidInput,
     GMTTypeError,
     GMTValueError,
 )
@@ -1465,8 +1464,7 @@ def virtualfile_from_vectors(self, vectors: Sequence) -> Generator[str, None, No
 
         rows = len(arrays[0])
         if not all(len(i) == rows for i in arrays):
-            msg = "All arrays must have same size."
-            raise GMTInvalidInput(msg)
+            raise GMTValueError(arrays, reason="All arrays must have same size.")
 
         family = "GMT_IS_DATASET|GMT_VIA_VECTOR"
         geometry = "GMT_IS_POINT"
diff --git a/pygmt/tests/test_clib_virtualfile_from_vectors.py b/pygmt/tests/test_clib_virtualfile_from_vectors.py
index ec8ccf4fe13..77f73f8c29a 100644
--- a/pygmt/tests/test_clib_virtualfile_from_vectors.py
+++ b/pygmt/tests/test_clib_virtualfile_from_vectors.py
@@ -9,7 +9,7 @@
 import pytest
 from pygmt import clib
 from pygmt.clib.session import DTYPES_NUMERIC
-from pygmt.exceptions import GMTInvalidInput
+from pygmt.exceptions import GMTValueError
 from pygmt.helpers import GMTTempFile
 from pygmt.helpers.testing import skip_if_no
 
@@ -141,7 +141,7 @@ def test_virtualfile_from_vectors_diff_size():
     x = np.arange(5)
     y = np.arange(6)
     with clib.Session() as lib:
-        with pytest.raises(GMTInvalidInput):
+        with pytest.raises(GMTValueError):
             with lib.virtualfile_from_vectors((x, y)):
                 pass