Background: There is a lack of large studies on urinary (UI) and fecal incontinence (FI) following multiple sclerosis (MS) diagnosis. Thus, our goal was to investigate the association between MS and the incidence of UI and FI in patients followed up for up to 10 years in Germany. Methods: This study included patients who received an initial documentation of MS diagnosis in general practices in Germany during 2005–2018 (index date). Patients without MS were matched (1:1) to those with MS using propensity scores based on sex, age, index year, follow-up time (in years), general practice, and the Charlson Comorbidity Index score (index date: a randomly selected visit date). Results: This retrospective study included 4,461 patients with MS and 4,461 patients without MS (69.9% women; mean [SD] age 44.2 [12.7] years). Within 10 years of index date, a higher proportion of patients with MS were diagnosed with UI (11.7 vs. 3.2%) and FI (2.3 vs. 0.5%; p values <0.001) than those without MS. MS was further found to be associated with both UI (hazard ratio [HR] = 3.85) and FI (HR = 5.38; p values <0.001) in the Cox regressions. Conclusions: UI and FI are frequent complications of MS, and the presence of these complications should be regularly assessed in primary care practices.