Aim Our aim was to compare the long-term anatomical outcomes between robot-assisted ventral mesh rectopexy (RVMR) and laparoscopic ventral mesh rectopexy (LVMR) for external or internal rectal prolapse. Method This study is a follow-up of a single-centre randomized controlled trial (RCT). Thirty patients were randomly allocated to RVMR (n = 16) or LVMR (n = 14). The primary end-point was maintenance of the restored pelvic anatomy 5 years after the operation, as assessed by magnetic resonance (MR) defaecography. Secondary outcome measures included the Pelvic Organ Prolapse Quantification (POP-Q) measures and functional results assessed using symptom questionnaires. Results Twenty-six patients (14 RVMR and 12 LVMR) completed the 5-year follow-up and were included in the study. The MRI results, POP-Q measurements and symptom-specific quality of life measures did not differ between the RVMR and LVMR groups. The MRI measurements of the total study population remained unchanged between 3 months and 5 years. In the Pelvic Floor Distress Inventory (PFDI-20), the RVMR group had lower symptom scores (mean 96.0, SD 70.7) than the LVMR group (mean 160.6, SD 58.9; P = 0.004). In the subscales of pelvic organ prolapse (POPDI-6) (mean 23.2, SD 24.3 vs mean 52.4, SD 22.4; P = 0.001) and the Colorectal-Anal Distress Inventory (CRADI-8) (mean 38.4, SD 23.3 vs mean 58.6, SD 25.4; P = 0.009), the patients in the RVMR group had significantly better outcomes. Conclusion After VMR, the corrected anatomy was preserved. There were no clinically significant differences in anatomical results between the RVMR and LVMR procedures 5 years after surgery based on MR defaecography. However, functional outcomes were better after RMVR.