diff --git a/tests/performance_tests/test_cases/gpt/gpt_16b_perf/model_config.yaml b/tests/performance_tests/test_cases/gpt/gpt_16b_perf/model_config.yaml
index 9d016044481..c283965d0f7 100644
--- a/tests/performance_tests/test_cases/gpt/gpt_16b_perf/model_config.yaml
+++ b/tests/performance_tests/test_cases/gpt/gpt_16b_perf/model_config.yaml
@@ -20,9 +20,11 @@ BATCH_SIZES:
   - 8
   - 32
 TOLERANCE_PCT: 10
+# p99 omitted on purpose: with NUM_TIMED_ITERS=5 it is the max of 5 samples,
+# not a real percentile, so it produces flaky regressions even when throughput
+# / avg / p50 are stable. p99 is still recorded in results.json for visibility.
 METRICS:
   - throughput_tok_per_sec
   - avg_latency_ms
   - p50_latency_ms
-  - p99_latency_ms
   - tpot_ms_per_tok
diff --git a/tests/performance_tests/test_cases/gpt/gpt_583m_perf/model_config.yaml b/tests/performance_tests/test_cases/gpt/gpt_583m_perf/model_config.yaml
index b97c56bb0b3..fee8b9a8208 100644
--- a/tests/performance_tests/test_cases/gpt/gpt_583m_perf/model_config.yaml
+++ b/tests/performance_tests/test_cases/gpt/gpt_583m_perf/model_config.yaml
@@ -22,9 +22,11 @@ BATCH_SIZES:
   - 32
   - 128
 TOLERANCE_PCT: 10
+# p99 omitted on purpose: with NUM_TIMED_ITERS=5 it is the max of 5 samples,
+# not a real percentile, so it produces flaky regressions even when throughput
+# / avg / p50 are stable. p99 is still recorded in results.json for visibility.
 METRICS:
   - throughput_tok_per_sec
   - avg_latency_ms
   - p50_latency_ms
-  - p99_latency_ms
   - tpot_ms_per_tok
diff --git a/tests/performance_tests/test_cases/hybrid/hybrid_2b_perf/model_config.yaml b/tests/performance_tests/test_cases/hybrid/hybrid_2b_perf/model_config.yaml
index 04303bd2663..d884f4ef057 100644
--- a/tests/performance_tests/test_cases/hybrid/hybrid_2b_perf/model_config.yaml
+++ b/tests/performance_tests/test_cases/hybrid/hybrid_2b_perf/model_config.yaml
@@ -18,9 +18,11 @@ BATCH_SIZES:
   - 32
   - 128
 TOLERANCE_PCT: 10
+# p99 omitted on purpose: with NUM_TIMED_ITERS=5 it is the max of 5 samples,
+# not a real percentile, so it produces flaky regressions even when throughput
+# / avg / p50 are stable. p99 is still recorded in results.json for visibility.
 METRICS:
   - throughput_tok_per_sec
   - avg_latency_ms
   - p50_latency_ms
-  - p99_latency_ms
   - tpot_ms_per_tok