This systematic review and meta-analysis of randomized controlled trials tested the effects of home-based, supervised, or mixed exercise interventions on the functional capacity (FC) and quality of life (QoL) in colorectal cancer patients. A literature search was performed using the PubMed, Embase, Cochrane, and Medline databases. Two reviewers screened the literature through March 10, 2021 for studies related to exercise and colorectal cancer. Of the 1161 screened studies in the initial search, 13 studies met the eligibility criteria (home-based = 6 studies; supervised or mixed = 7 studies). Overall, 706 patients were enrolled in the trials, and 372 patients were submitted to home-based, supervised, or mixed exercise intervention. The overall results from the main meta-analysis showed a significant effect regarding supervised or mixed intervention (6 studies; p = 0.002; I2 = 43%; PI 0.41–1.39); however, no significant effect was observed for home-based intervention (5 studies; p = 0.05; I2 = 25%; PI − 0.34–0.76). A sensitivity analysis based on studies with intervention adherence ≥ 80% (home-based = 3 studies; supervised or mixed = 4 studies) revealed that home-based intervention or intervention entirely supervised or with some level of supervision (mixed) are effective in improving the QoL and FC of CRC patients. In summary, this meta-analysis verified that supervised and home-based exercise can modify QoL and FC when intervention adherence ≥ 80%. Regardless of the supervision characteristics, future RCTs are strongly encouraged to provide a detailed description of the exercise variables in physical interventions for CRC prescription. This perspective will allow a refined exercise prescription for patients with CRC, mainly according to their clinical status.