FITNESSGRAM® is the most widely used criterion-referenced tool to assess/report on student health-related fitness across the US. Potential weight-related biases with the two most common tests of musculoskeletal fitness-the trunk extension and Back-Saver Sit-and-Reach (sit-and-reach)-have been hypothesized, though have not been studied. To determine the association between musculoskeletal fitness test performance and weight status, we use data from 571,133 New York City public school 4th-12th grade students (85% non-White; 75% qualified for free or reduced-price meals) with valid/complete 2017-18 FITNESSGRAM® data. Adjusted logistic mixed effects models with a random effect for school examined the association between weight status and whether a student was in the Healthy Fitness Zone (HFZ; met sex- and age-specific criterion-referenced standards) for the trunk extension and sit-and-reach. Compared to students with normal weight, the odds of being in the HFZ for trunk extension were lower for students with underweight (OR = 0.77; 95% CI: 0.741, 0.795) and higher for students with overweight (OR = 1.10; 95% CI: 1.081, 1.122) and obesity (OR = 1.11; 95% CI: 1.090, 1.13). The odds of being in the HFZ for sit-and-reach were lower for students with underweight OR = 0.85; 95% CI: 0.826, 0.878), overweight (OR = 0.83; 95% CI: 0.819, 0.844) and obesity (OR = 0.65; 95% CI: 0.641, 0.661). Students with overweight and obesity perform better on the trunk extension, yet worse on the sit-and-reach, compared to students with normal weight. Teachers, administrators, and researchers should be aware of the relationship of BMI with student performance in these assessments.