Objectives: This study aimed to compare the effects of facility-based and home-based exercise prehabilitation on postoperative functional capacity and postoperative outcomes in patients undergoing gastrointestinal cancer surgery using a network meta-analysis. Methods: This systematic review and network meta-analysis included randomized controlled trials of exercise-based prehabilitation in patients undergoing gastrointestinal cancer surgery. Facility-based and home-based exercise interventions were compared using random-effects models to evaluate postoperative functional capacity, overall complications, and length of stay. Certainty of evidence was assessed using the CINeMA framework. Results: Nine randomized controlled trials were included. Exercise-based prehabilitation significantly improved postoperative functional capacity compared with control in pairwise meta-analysis (MD = 26.10 m; 95% CI 4.59 to 47.62). In network meta-analysis, facility-based exercise prehabilitation significantly improved postoperative functional capacity compared with control (MD = 24.11 m; 95% CI 2.01 to 46.22), whereas home-based prehabilitation showed no statistically significant effect (MD = 32.12 m; 95% CI −1.70 to 65.93). Conclusions: This study suggests that exercise prehabilitation may be an effective strategy for improving or preserving postoperative functional capacity in patients undergoing gastrointestinal cancer surgery, with facility-based exercise prehabilitation showing more consistent and statistically significant effects.