diff --git a/CHANGELOG.md b/CHANGELOG.md
index b3832ab2b..e027df9ad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## 0.11.2dev
 
+* [Fix] Handle empty SQL statements gracefully (#1066)
+
 ## 0.11.1 (2025-03-25)
 
 * [Fix] No longer showing the Slack link in error messages
diff --git a/src/sql/run/run.py b/src/sql/run/run.py
index a1e34aa7d..8513bf135 100644
--- a/src/sql/run/run.py
+++ b/src/sql/run/run.py
@@ -29,18 +29,30 @@ def run_statements(conn, sql, config, parameters=None):
     .. literalinclude:: ../../examples/run_statements.py
 
     """
-    if not sql.strip():
+    # First, try to extract the usable SQL statements without comments
+    statements = list(
+        filter(
+            None,
+            map(
+                lambda stmt: sqlparse.format(stmt, strip_comments=True),
+                sqlparse.split(sql),
+            ),
+        )
+    )
+
+    # Handle the empty SQL case
+    if not sql.strip() or not statements:
         return "Connected: %s" % conn.name
 
-    for statement in sqlparse.split(sql):
-        # strip all comments from sql
-        statement = sqlparse.format(statement, strip_comments=True)
-        # trailing comment after semicolon can be confused as its own statement,
-        # so we ignore it here.
-        if not statement:
+    # Ensure we have some return value. This maintains type checkers happy
+    result = None
+    statement = None
+
+    for statement in statements:
+        if not statement.strip():
             continue
 
-        first_word = sql.strip().split()[0].lower()
+        first_word = statement.strip().split()[0].lower()
 
         if first_word == "begin":
             raise exceptions.RuntimeError("JupySQL does not support transactions")
diff --git a/src/tests/test_magic.py b/src/tests/test_magic.py
index c0ee3c357..b5865c1fe 100644
--- a/src/tests/test_magic.py
+++ b/src/tests/test_magic.py
@@ -1221,7 +1221,7 @@ def test_error_on_invalid_connection_string_with_possible_typo(ip_empty, clean_c
 """  # noqa
 
 invalid_connection_string_duckdb_bottom = f"""
-Perhaps you meant to use the 'duckdb' db 
+Perhaps you meant to use the 'duckdb' db
 To find more information regarding connection: https://jupysql.ploomber.io/en/latest/integrations/duckdb.html
 
 To fix it:
@@ -1783,7 +1783,7 @@ def test_error_when_using_section_argument_but_values_are_invalid(ip_empty, tmp_
     with pytest.raises(UsageError) as excinfo:
         ip_empty.run_cell("%sql --section section")
 
-    message = "Could not parse SQLAlchemy URL from string 'not-a-driver://'"
+    message = "Could not parse SQLAlchemy URL from given URL string"
     assert message in str(excinfo.value)
 
 
diff --git a/src/tests/test_run.py b/src/tests/test_run.py
index 6557c1540..7f25cc25e 100644
--- a/src/tests/test_run.py
+++ b/src/tests/test_run.py
@@ -108,6 +108,13 @@ def test_sql_is_empty(mock_conns):
     assert run_statements(mock_conns, "  ", Config) == "Connected: %s" % mock_conns.name
 
 
+def test_sql_comment_only(mock_conns):
+    assert (
+        run_statements(mock_conns, "-- this is a comment", Config)
+        == "Connected: %s" % mock_conns.name
+    )
+
+
 @pytest.mark.parametrize(
     "connection",
     [