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Intraductal papillary mucinous neoplasms (IPMNs) resection margins are assessed intraoperatively using frozen section (IFS) pathology. We conducted a systematic review to evaluate the concordance of IFS with permanent histopathology and the association between IFS margin status and recurrence. A systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We queried PubMed, Embase, Scopus, and Google Scholar for studies reporting IFS in patients undergoing resection for IPMN. Data, including IFS margin status, recurrence rates, and final pathology, were extracted. Positive margins were defined as high-grade dysplasia or invasive cancer. Seven studies, with a total of 706 patients, met the inclusion criteria. Positive IFS margins were reported in 9.4% of cases, with a high correlation (98%) between IFS and final pathology. Recurrence occurred in 15.4% of patients. Fifty-nine of 85 (69.4%) patients with recurrence of IPMN or intraductal papillary mucinous carcinoma (IPMC) had negative IFS margins. IFS accurately predicts final pathology and is a valuable tool for guiding intraoperative decision-making. A sizeable number of patients experienced recurrence despite negative margins, highlighting the need for adjunct diagnostic modalities and continued surveillance following resection, regardless of margin status.