Purpose: Recurrence after resection of pancreatic mucinous cystic neoplasms (MCN) and intraductal papillary mucinous neoplasms (IPMN) is often due to residual disease at the margin. The prognostic value of histopathological and molecular features at the resection margin remains unclear. This study aimed to evaluate associations between margin features (dysplasia grade, residual IPMN/MCN, and molecular markers KRAS, GNAS, RNF43, TP53) and recurrence risk. Methodology: Systematic review and meta-analysis of PubMed, Embase, and Web of Science from 1960 to November 2025 for English-language cohort studies reporting recurrence by final margin histopathology and/or molecular profile in resected IPMN or MCN. Pooled odds ratios (OR) using random-effects model; certainty graded via GRADE approach. Results: Thirty-nine studies (n=8,214 patients) were included. High-grade dysplasia at the margin increased recurrence risk (OR 5.52, 95% CI 4.01–7.60; 31 studies). Residual IPMN/MCN without dysplasia conferred OR 2.78 (95% CI 2.15–3.59). Molecular markers: KRAS mutation OR 4.87 (95% CI 3.22–7.36; 12 studies), GNAS OR 3.91 (95% CI 2.44–6.27; 9 studies), TP53 mutation predicted progression to carcinoma (OR 8.14, 95% CI 4.10–16.15). Five-year recurrence rates: 47% (high-grade dysplasia + KRAS mutation) versus 12% (negative margins). Conclusion: High-grade dysplasia and KRAS/GNAS mutations at resection margins are strong independent predictors of recurrence in MCN and IPMN. Molecular margin assessment may guide decisions on re-resection or intensified surveillance.