Background: Nonalcoholic fatty liver disease (NAFLD) is associated with several comorbidities like obesity, diabetes, cardiovascular diseases, cirrhosis, and hepatocellular carcinoma. The relationship between polypharmacy and Health-related Quality of Life (QoL) in pediatrics with NAFLD remains unclear. The objectives of this study were to examine the association between polypharmacy and health related QoL, and to explore predictors that affect QoL, in pediatric patients diagnosed with NAFLD. Methods: A Retrospective multicenter observational study was conducted to evaluate the QoL in pediatric patients with polypharmacy defined as using two or more medications using baseline patients’ data from two Nonalcoholic Steatohepatitis Clinical Research Network (NASH) studies. Comparing QoL between polypharmacy versus non-polypharmacy groups was analyzed by using student’s t-test. Multivariable linear models were performed on each QoL domain of parent-proxy and child-self reports. Results: The data included 358 children who met the inclusion criteria; 273 met the definition for polypharmacy. The mean age was 12.81 ± 2.35 years (range 7-17). Of all patients, 256 (71.5%) were males. Patients in non-polypharmacy group had a significant (p < 0.05) higher QoL compared with patients in polypharmacy group in emotional, social, and school functioning scores (60.7 vs 70.5, 65.9 vs 73.8, 59.1 vs 64.8 respectively in parent-proxy scores and 66.8 vs 76.8, 73.5 vs 81.2, 63.6 vs 70.6 respectively in child-self scores). Psychosocial health summary score was significantly higher in non-polypharmacy group (61.9 vs 69.7 in parent-proxy scores and 67.9 vs 76.2 in child-self scores, both p < 0.01). Number of medications had a significant negative impact on psychosocial health summary score of parents and children QoL survey (B = -1.7 and -1.9 respectively, both p < 0.01). It also negatively affected the children’s survey of physical health summary score (B = -1.6, p < 0.01). Conclusion: Pediatrics patients diagnosed with NAFLD on two or more medications have lower QoL than NAFLD pediatrics without polypharmacy. A decrease in QoL was more noticeable in psychological health domains of parent-proxy and child-self QoL reports.