Pulmonary embolism (PE) is associated with atrial fibrillation (AF). This study sought to explore if the CHADS (2) score could predict the prognosis of PE in patients with AF. In a tertiary hospital, 4,288 consecutive patients with diagnosis of PE were screened. In total, 305 patients with PE had AF and were included in this retrospective study. In-hospital outcome was defined as at least one of the following: death from any cause, need for intravenous catecholamine administration, endotracheal intubation, cardiopulmonary resuscitation, or thrombolytic therapy. The in-hospital outcome occurred in 10.2% of the patients. Patients with adverse outcome had higher CHADS (2) score, CHA (2) DS (2) -VASc score, and simplified pulmonary embolism severity index (sPESI) score. The area under the receiver operating characteristics curve was 0.66, 0.62, and 0.71 for CHADS (2) score, CHA (2) DS (2) -VASc score, and sPESI score, respectively, in predicting in-hospital outcome. The incidence of in-hospital outcome was 3.4 and 14.4% in sPESI=0 and sPESI 1 groups ( p <0.01). CHADS (2) also had good predictive value with the incidence of in-hospital outcome, being 4.6% in CHADS (2) <2 and 14.3% in CHADS (2) 2 groups ( p <0.01). The incidences of in-hospital outcome were 2.6, 4.8, 7.4, and 17.3% in patients with sPESI=0 and CHADS (2) <2, sPESI=0 and CHADS (2) 2, sPESI1 and CHADS (2) <2, and sPESI1 and CHADS (2) 2 ( p <0.01), respectively. In multivariable analysis, CHADS (2) (odds ratio: 1.50; 95% confidence interval: 1.11-2.02; p <0.01) was an independent predictor of in-hospital adverse outcome. High CHADS (2) score could predict worse in-hospital outcome in patients with PE and AF.