Background: The aim of the present study was to compare sacral nerve stimulation (SNS) for constipation (SNS-C) with SNS for idiopathic faecal incontinence (SNS-IFI) regarding explantation rate, additional visits, and improvement of patient satisfaction 5 years after implantation. Methods: From our prospective database (launched in 2009), we extracted all SNS-C patients 5 years post-implantation, and the SNS-IFI patients implanted just before and just after each SNS-C patient. We retrospectively evaluated the explantation rate, number of additional visits, and patient satisfaction using a visual analogue scale (VAS). We hypothesized that compared with those in the SNS-IFI group: (1) the explantation rate would be higher in SNS-C patients, (2) the number of additional visits would be higher in SNS-C patients, and (3) in patients with an active implant at 5 years, the improvement in VAS would be the same. Results: We included 40 SNS-C patients and 80 SNS-IFI patients. In the SNS-C group 7/40 (17.5%), patients were explanted, compared to 10/80 (12.5%) patients in the SNS-IFI group (p = 0.56). The mean number of additional visits in the SNS-C group was 3.5 (95% CI 2.8–4.1)) and 3.0 (95% CI 2.6–3.6)) in the SNS-IFI group (p = 0.38). Additional visits due to loss of efficacy were significantly higher in the SNS-C patients (p = 0.03). The reduction in VAS score (delta VAS) at 5 years was 37.1 (95% CI 20.9–53.3) in the SNS-C group, and 46.0 (95% CI 37.9–54.0) in the SNS-IFI group (p = 0.27). Conclusions: No significant difference was found regarding explantation rate, number of additional visits, or improvement of VAS at 5 years after SNS implantation between SNS-C patients and SNS-IFI patients.