Atrial fibrillation (AF) may increase the risk of thromboembolic (TE) complications in patients with left ventricular assist devices (LVADs). In a single-center study, we investigated 205 patients with sinus rhythm (SR group) and 117 patients with AF (AF group). Our main read outs were 2 year overall survival (primary end point), perioperative right heart failure (RHF), and 2 year freedom from stroke, pump thrombosis, and gastrointestinal bleeding (secondary end points). Oral anticoagulation was performed with phenprocoumon (international normalized ratio target range: 2.3–2.8) and aspirin (100 mg/day). Propensity score (PS) adjustment was used for statistical analysis. Two year survival was 65.4% (n = 134) in the SR group and 51.3% (n = 60) in the AF group. The PS-adjusted hazard ratio (HR) of 2 year mortality was higher in the AF group than in the SR group (HR = 1.48 [95% confidence interval (CI): 1.02–2.15; p = 0.038]). Right heart failure was a more frequent cause of death in the AF group than in the SR group (p = 0.008). The PS-adjusted odds ratio of perioperative RHF was for the AF group (reference: SR group) 1.32 (95% CI: 0.80–2.18; p = 0.280). The PS-adjusted 2 year HRs of TE and bleeding events were comparable between both groups and were for stroke, pump thrombosis, and gastrointestinal bleeding (reference: SR group) 0.90 (95% CI: 0.53–1.55; p = 0.714), 0.76 (95% CI: 0.14–4.31; p = 0.639), and 1.01 (95% CI: 0.60–1.70; p = 0.978), respectively. Our data indicate that AF increases midterm mortality, but does not influence the risk of stroke, pump thrombosis, and gastrointestinal bleeding. The higher midterm mortality in AF patients is most likely disease-related and should have no influence on LVAD implantation.