diff --git a/python/scripts/nvbench_compare.py b/python/scripts/nvbench_compare.py
index 0d29a04..5afa28a 100644
--- a/python/scripts/nvbench_compare.py
+++ b/python/scripts/nvbench_compare.py
@@ -3179,7 +3179,7 @@ def main() -> int:
         type=float,
         dest="threshold",
         default=0.0,
-        help="only show benchmarks where percentage diff is >= THRESHOLD",
+        help="only show rows where abs(%%Diff) is >= THRESHOLD percent",
     )
     parser.add_argument(
         "--preset",
@@ -3373,7 +3373,7 @@ def main() -> int:
                 run_data,
                 ref_root["benchmarks"],
                 cmp_root["benchmarks"],
-                threshold=args.threshold,
+                threshold=args.threshold / 100.0,
                 plot_along=args.plot_along,
                 plot=args.plot,
                 dark=args.dark,
diff --git a/python/test/test_nvbench_compare.py b/python/test/test_nvbench_compare.py
index cd40398..92221fa 100644
--- a/python/test/test_nvbench_compare.py
+++ b/python/test/test_nvbench_compare.py
@@ -2961,3 +2961,34 @@ def test_main_passes_selected_preset_to_compare_benches(monkeypatch, nvbench_com
         "comparison_thresholds"
     ] == nvbench_compare.get_comparison_thresholds("strict")
     assert captured["display"] == "explain"
+
+
+def test_main_converts_threshold_diff_percent_to_fraction(monkeypatch, nvbench_compare):
+    devices = [{"id": 0, "name": "Test GPU"}]
+    root = {
+        "devices": devices,
+        "benchmarks": [],
+    }
+    captured = {}
+
+    monkeypatch.setattr(nvbench_compare.reader, "read_file", lambda _: root)
+
+    def fake_compare_benches(*args, **kwargs):
+        del args
+        captured["threshold"] = kwargs["threshold"]
+
+    monkeypatch.setattr(nvbench_compare, "compare_benches", fake_compare_benches)
+    monkeypatch.setattr(
+        sys,
+        "argv",
+        [
+            "nvbench_compare",
+            "--threshold-diff",
+            "5",
+            "ref.json",
+            "cmp.json",
+        ],
+    )
+
+    assert nvbench_compare.main() == 0
+    assert captured["threshold"] == pytest.approx(0.05)