Purpose The purpose of this study is to analyze an algorithm intended to prevent incomplete pyloromyotomy in 3-port laparoscopic (3TP) and laparoendoscopic single-site (LESS-P) procedures in a teaching hospital. Methods We defined the pyloroduodenal and pyloroantral junctions as anatomical margins prior pyloromyotomy by palpating and coagulating the serosa with the hook cautery instrument. Incomplete pyloromyotomies, mucosa perforations, serosa lacerations, and wound infections were recorded for pediatric surgical trainees (PST) and board-certified pediatric surgeons (BC). Results We reviewed the medical files of 233 infants, who underwent LESS-P (n = 21), 3TP (n = 71), and open pyloromyotomy (OP, n = 141). No incomplete pyloromyotomies occurred. In contrast to OP, mucosa perforations did not occur in the laparoscopic procedures during the study period (6.38% vs. 0%, P =.013). OP had insignificantly more serosal lacerations (3.5% vs. 1.4%, P =.407). There was no difference in the rate of wound infections between OP and laparoscopic procedures (2.8% vs. 4.3%, P =.715). In the latter, all wound infections were associated with the use of skin adhesive. Conclusions This algorithm helps avoiding incomplete laparoscopic pyloromyotomy during the learning curve and in a teaching setting. It is not risky to assist 3TP and LESS-P to PST as this led to a decreased rate of mucosa perforations without experiencing incomplete pyloromyotomies.