Background/objectives: To analyze risk factors for prolonged operative time (OT) in patients undergoing rectal cancer surgery, and to explore the effects of prolonged OT on immediate surgical outcomes and long-term oncological outcomes. Methods: A single-center retrospective review of all patients who underwent an elective rectal resection for primary rectal adenocarcinoma between 2010 and 2020. OT was standardized according to surgeon-specific and surgical approach-specific median values. Subsequently, the cohort was divided according to surgery duration: The Short OT group (244 patients; median OT 201 min, range 46–600) and the Long OT group (250 patients; median OT 340 min, range 145–960). Results: Multivariate analysis identified independent predictors for prolonged surgery: higher BMI (AOR 1.07, p = 0.002) and distance from anal verge (AOR 0.89, p < 0.001). Intraoperative complications occurred more frequently in the Long OT group (21.6% vs. 10.2%, p < 0.001), as did overall post-operative morbidity (73.2% vs. 60.7%, p = 0.003). The 5-year OS rates were comparable between groups (88.8% vs. 90.8%, p = 0.14); however, 5-year RFS was significantly worse in the Long OT group (65.5% vs. 78.2%, p = 0.004). Multivariable Cox regression using surgeon–approach standardized time quartiles showed reduced recurrence-free survival per one-quartile duration increase (HR 1.37, 95% CI 1.12–1.69, p = 0.002). Conclusions: Higher BMI and lower tumor location were found to be independent preoperative predictors of prolonged rectal cancer surgery. Prolonged operative time was associated with higher perioperative morbidity and poorer long-term recurrence-free survival.