diff --git a/python/scripts/nvbench_compare.py b/python/scripts/nvbench_compare.py
index c96a4d4..e75f158 100644
--- a/python/scripts/nvbench_compare.py
+++ b/python/scripts/nvbench_compare.py
@@ -102,6 +102,16 @@ def read_nvbench_json_root(filename: str) -> Mapping[str, Any]:
     return root
 
 
+def format_json_structure_error(ref: str, comp: str, exc: Exception) -> str:
+    if isinstance(exc, KeyError) and exc.args:
+        detail = f"missing key {exc.args[0]!r}"
+    else:
+        detail = str(exc) or exc.__class__.__name__
+    return (
+        f"invalid NVBench JSON structure while comparing {ref!r} and {comp!r}: {detail}"
+    )
+
+
 # These dataclasses are treated as parsed value objects. frozen=True prevents
 # accidental field reassignment but does not imply deep immutability.
 
@@ -3186,6 +3196,9 @@ def main() -> int:
         except ValueError as exc:
             print(str(exc))
             return 1
+        except (KeyError, TypeError, IndexError) as exc:
+            print(format_json_structure_error(ref, comp, exc))
+            return 1
 
         if len(selected_ref_devices) != len(selected_cmp_devices):
             print(
@@ -3240,6 +3253,9 @@ def main() -> int:
         except ValueError as exc:
             print(str(exc))
             return 1
+        except (KeyError, TypeError, IndexError) as exc:
+            print(format_json_structure_error(ref, comp, exc))
+            return 1
 
     print("# Summary\n")
     print(f"- Total Matches: {stats.config_count}")
diff --git a/python/test/test_nvbench_compare.py b/python/test/test_nvbench_compare.py
index 8ef9a05..0743544 100644
--- a/python/test/test_nvbench_compare.py
+++ b/python/test/test_nvbench_compare.py
@@ -2265,6 +2265,50 @@ def test_main_rejects_non_object_root_array_entries(
     )
 
 
+def test_main_reports_invalid_device_entry_structure(
+    monkeypatch, capsys, nvbench_compare
+):
+    monkeypatch.setattr(
+        nvbench_compare.reader,
+        "read_file",
+        lambda _: {"devices": [{}], "benchmarks": []},
+    )
+    monkeypatch.setattr(
+        sys,
+        "argv",
+        [
+            "nvbench_compare",
+            "--reference-devices",
+            "0",
+            "--compare-devices",
+            "0",
+            "ref.json",
+            "cmp.json",
+        ],
+    )
+
+    assert nvbench_compare.main() == 1
+    output = capsys.readouterr().out
+    assert "invalid NVBench JSON structure" in output
+    assert "missing key 'id'" in output
+
+
+def test_main_reports_invalid_benchmark_entry_structure(
+    monkeypatch, capsys, nvbench_compare
+):
+    monkeypatch.setattr(
+        nvbench_compare.reader,
+        "read_file",
+        lambda _: {"devices": [], "benchmarks": [{}]},
+    )
+    monkeypatch.setattr(sys, "argv", ["nvbench_compare", "ref.json", "cmp.json"])
+
+    assert nvbench_compare.main() == 1
+    output = capsys.readouterr().out
+    assert "invalid NVBench JSON structure" in output
+    assert "missing key 'name'" in output
+
+
 def test_main_prints_bulk_debug_python_to_stdout(monkeypatch, capsys, nvbench_compare):
     devices = [{"id": 0, "name": "Test GPU"}]
     root = {