Background: Hemodialysis (HD) and peritoneal dialysis (PD) are deemed medically equivalent for therapy of end-stage renal disease (ESRD) and reimbursed by the German statutory health insurance (SHI). However, although the home dialysis modality PD is associated with higher patient autonomy than HD, for unknown reasons, PD uptake is low in Germany. Hence, we compared HD with PD regarding health economic outcomes, particularly costs, as potentially relevant factors for the predominance of HD. Methods: Claims data from two German health insurance funds were analysed in a retrospective cohort study regarding the prevalence of HD and PD in 2013–2016. Propensity score matching created comparable HD and PD groups (n = 436 each). Direct annual health care costs were compared. A sensitivity analysis included a comparison of different matching techniques and consideration of transportation costs. Additionally, hospitalisation and survival were investigated using Poisson regression and Kaplan-Meier curves. Results: Total direct annual average costs were higher for HD (€47,501) than for PD (€46,235), but not significantly (p = 0.557). The additional consideration of transportation costs revealed an annual cost advantage of €7000 for PD. HD and PD differed non-significantly in terms of hospitalisation and survival rates (p = 0.610/p = 0.207). Conclusions: PD has a slight non-significant cost advantage over HD, especially when considering transportation costs.