Glycopyrrolate premedication is used for pediatric upper endoscopy procedures, with limited clinical evidence for efficacy. We investigated whether glycopyrrolate use is associated with lower incidence of procedure-related events and serious adverse events (SAEs) using the Pediatric Sedation Research Consortium registry. Pediatric upper endoscopy procedures performed between April 27, 2020 and February 3, 2022 were included (N = 1046). The primary outcome was the incidence of any procedure-related events during induction, maintenance, or recovery, and the secondary outcome was incidence of SAEs. The event rate was 15%, including 30 SAEs (3%). On multivariable analysis, glycopyrrolate was not associated with the overall event rate (odds ratio [OR]: 1.08; 95% confidence interval [CI]: 0.72, 1.61), but was associated with lower odds of SAEs (OR: 0.34; 95% CI: 0.13, 0.91). Although glycopyrrolate was associated with lower odds of SAEs after accounting for patient and procedure characteristics, validation through prospective trials is needed to support its routine use in clinical practice.