diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py
index 31ae78f5ad..29b5d2c7b5 100755
--- a/python/ctsm/site_and_regional/neon_site.py
+++ b/python/ctsm/site_and_regional/neon_site.py
@@ -18,6 +18,7 @@
 # pylint: disable=wrong-import-position, import-error, unused-import, wrong-import-order
 from ctsm import add_cime_to_path
 from ctsm.path_utils import path_to_ctsm_root
+from ctsm.utils import abort
 
 from CIME import build
 from CIME.case import Case
@@ -75,6 +76,9 @@ def build_base_case(
 
         if overwrite and os.path.isdir(case_path):
             print("Removing the existing case at: {}".format(case_path))
+            if os.getcwd() == case_path:
+               abort("Trying to remove the directory tree that we are in")
+
             shutil.rmtree(case_path)
 
         with Case(case_path, read_only=False) as case:
@@ -211,6 +215,8 @@ def run_case(
         if os.path.isdir(case_root):
             if overwrite:
                 print("---- removing the existing case -------")
+                if os.getcwd() == case_root:
+                   abort("Trying to remove the directory tree that we are in")
                 shutil.rmtree(case_root)
             elif rerun:
                 with Case(case_root, read_only=False) as case: