diff --git a/cvise/passes/lines.py b/cvise/passes/lines.py
index f61e449d7..ddeedf093 100644
--- a/cvise/passes/lines.py
+++ b/cvise/passes/lines.py
@@ -39,11 +39,18 @@ def generate_hints(self, test_case: Path, process_event_notifier: ProcessEventNo
     def _generate_hints_for_text_lines(self, input_path: Path, path_id: int | None, hints: list[Hint]) -> None:
         """Generate a hint per each line in the input as written."""
         with open(input_path, 'rb') as in_file:
+            lines = in_file.readlines()
             file_pos = 0
-            for line in in_file:
+            for i, line in enumerate(lines):
                 end_pos = file_pos + len(line)
-                hints.append(Hint(patches=(Patch(left=file_pos, right=end_pos, path=path_id),)))
-                file_pos = end_pos
+
+                # Do not consume the file-terminating newline.
+                if i == len(lines) - 1 and line.endswith(b'\n'):
+                    end_pos -= 1
+
+                if end_pos > file_pos:
+                    hints.append(Hint(patches=(Patch(left=file_pos, right=end_pos, path=path_id),)))
+                file_pos += len(line)
 
     def _generate_topformflat_hints(
         self,
diff --git a/cvise/tests/test_lines.py b/cvise/tests/test_lines.py
index 929c34f9c..f61c3fb0b 100644
--- a/cvise/tests/test_lines.py
+++ b/cvise/tests/test_lines.py
@@ -56,6 +56,19 @@ def is_valid_brace_sequence(s: bytes) -> bool:
     return balance == 0
 
 
+def test_trailing_newline_preserved(tmp_path: Path, input_path: Path):
+    """Test that removing the last line doesn't eat the trailing newline."""
+    input_path.write_bytes(b'int x = 2;\nint main() {\n}\n')
+    p, state = init_pass('None', tmp_path, input_path)
+    all_transforms = collect_all_transforms(p, state, input_path)
+
+    for transform in all_transforms:
+        assert transform.endswith(b'\n')
+
+    # Deleting the last line `}\n` now leaves the `\n` behind.
+    assert b'int x = 2;\nint main() {\n\n' in all_transforms
+
+
 def test_func_namespace_level0(tmp_path: Path, input_path: Path):
     """Test that arg=0 deletes top-level functions and namespaces."""
     input_path.write_text(
@@ -808,10 +821,10 @@ def test_multi_file_arg_none(tmp_path: Path):
     all_transforms = collect_all_transforms_dir(p, state, input_dir)
 
     assert (('bar.h', b'x = 1;\n'), ('foo.cc', b'char\nbar() {}\n')) in all_transforms
-    assert (('bar.h', b'int\n'), ('foo.cc', b'char\nbar() {}\n')) in all_transforms
+    assert (('bar.h', b'int\n\n'), ('foo.cc', b'char\nbar() {}\n')) in all_transforms
     assert (('bar.h', b'int\nx = 1;\n'), ('foo.cc', b'bar() {}\n')) in all_transforms
-    assert (('bar.h', b'int\nx = 1;\n'), ('foo.cc', b'char\n')) in all_transforms
-    assert (('bar.h', b''), ('foo.cc', b'')) in all_transforms
+    assert (('bar.h', b'int\nx = 1;\n'), ('foo.cc', b'char\n\n')) in all_transforms
+    assert (('bar.h', b'\n'), ('foo.cc', b'\n')) in all_transforms
 
 
 def test_multi_file_arg_0(tmp_path: Path):