Lower esophageal sphincter achalasia is associated with a higher risk of aspiration during anesthesia. Endoluminal Functional Lumen Imaging Probe (EndoFLIP) is used as an adjunctive tool in both the diagnosis and treatment of achalasia, for which all children require anesthesia. Anesthesia may affect the parameters of the EndoFLIP due to its effect on gut motility. There are no standard anesthesia protocols to help decrease the risk of aspiration and the undesirable effect of anesthesia on EndoFLIP parameters. This study aims to standardize an anesthesia protocol to target both goals. A protocol was developed to address perioperative management in patients undergoing EndoFLIP for any indication to minimize both anesthetic effect on the esophageal motility as well as perioperative complications. A retrospective data analysis was conducted on patients who underwent EndoFLIP at Cincinnati Children's Hospital Medical Center; pre- and post-protocol implementation data including adverse events was compared. Pre-protocol implementation: 60 cases (median age of 13.8 years, 30 [50%] females) with 2 cases of adverse events (3.3%). Post-protocol implementation: 71 cases (median age of 14.6 years, 37 [52.1%] females) with no adverse events (0/71 = 0%). In comparison between pre- and post-protocol cases, no significant difference was noted in gender, age, and adverse events. Post-protocol procedures were found to be significantly shorter (median time of 89 vs. 79 min, p = 0.004). Our anesthesia protocol provides a standardized way of administering anesthesia minimizing impact on EndoFLIP parameters and aspiration for patients with achalasia.