An accurate assessment of kidney function prior to hematopoietic cell transplantation (HCT) can help to properly dose conditioning chemotherapy and follow patients for the development of chronic kidney disease. We cross-sectionally examined 94 children and young adults prior to HCT to compare formal nuclear GFR testing with estimated GFR using creatinine and cystatin C-based equations including the original Schwartz formula and the more recent formulas developed in the Chronic Kidney Disease in Children (CKiD) cohort. The median age of the cohort was 5.9 years (range 0.26–30.5 years). The mean cohort nuclear GFR was 107.4 ± 24.7 ml/min/1.73m2, with 18/94 (19.1%) subjects having abnormal kidney function (GFR <90 ml/min/1.73m2) prior to HCT. The creatinine-based original Schwartz and bedside CKiD formulas showed significant bias (95% confidence interval), overestimating the nuclear GFR by 57.4 (49.0–65.8) and 14.1 (7.1–21.1) ml/min/1.73m2, respectively. Cystatin C formulas had less mean bias and improved accuracy, but also had decreased sensitivity to detect abnormal kidney function prior to HCT. The Full CKiD equation showed the best performance, with a mean bias of −3.6 (−8.4–1.2) ml/min/1.73m2 that was not significantly different from the measured value and 87.7% of estimates within ±30% of the nuclear GFR. While the more recent bedside CKiD formula performed better than the original Schwartz formula, both formulas had poor sensitivity for detecting a low GFR. An abnormal pre-transplant nuclear GFR was not associated with post-HCT acute kidney injury, the need for dialysis, or death in the first 100 days. In conclusion, we observed cystatin C-based equations outperformed creatinine-based equations in estimating GFR in children prior to HCT. However, all formulas had decreased sensitivity to detect impaired GFR. Formal measurement of kidney function should be considered in children and young adults who need an accurate assessment of kidney function prior to HCT.