Objectives The utility of frozen section evaluation of the pancreatic parenchymal resection margin(s) in the surgical management of intraductal papillary mucinous neoplasm (IPMN) remains controversial. We investigated the frequency of its use in IPMN resections and its impact on achievement of negative final parenchymal margin(s). Methods Sixty-two IPMN resections (11 with invasive carcinoma) performed over a 12-year period were studied. Results Frozen sections of the parenchymal margin(s) were performed on 44 of the 62 resections (71%), 30 (68%) of which had 10 positive and 22 indefinite margins on frozen section. Additional margin resections were performed in 14 of these 30 cases (47%), boosting the complete resection rate from 14% (2 of 14) on the initial margin(s) to 71% (10 of 14) on the final margin(s) (P = 0.002). Overall, negative final parenchymal margin(s) were achieved more frequently when evaluation of the initial margin(s) by frozen section was performed (35 of 44; 80%) than when it was not (11 of 18; 61%) (P = 0.13). Conclusions In the intraoperative management of IPMN, frozen sections are highly reliable for margin evaluation and are useful for guiding the extent of pancreatic resection.