Objectives: Pneumonia is related to poor prognosis in acute ischemic stroke (AIS), and its risk might be higher in atrial fibrillation (AF) related AIS with elevated plasma D-dimer. The aim of our study was to investigate the prognostic value of D-dimer for predicting clinical outcome of AF-related AIS with pneumonia. Method: AF-related AIS patients with pneumonia were prospectively enrolled. Receiver operating characteristic (ROC) curve was used to determine the optimal D-dimer point for 3-month mortality and death/severe disability. The associations between the D-dimer and 3-month mortality and death/severe disability were assessed by multivariable logistic regression analysis. Results: A total of 415 patients were enrolled in this study. ROC curve analysis showed that the optimal cut point of D-dimer for 3-month death/severe disability and mortality were D-dimer≥2.35mg/l and D-dimer≥3.35mg/l, respectively. Multivariable logistic regression analysis showed that D-dimer≥2.35mg/l(OR 5.95, 95% CI: 3.09-11.45, P<0.001), higher NIHISS score(OR:1.53, 95% CI: 1.38–1.68, P<0.001) were associated with increased risk of 3-month death/severe disability), and anticoagulant was associated with decreased risk of death/severe disability (OR:0.16, 95% CI: 0.07-0.35, P<0.001). Higher NIHISS score(OR:1.56, 95% CI: 1. .37–1.77, P<0.001), higher age(OR 1.06, 95% CI: 1.01–1.11, P=0.019), D-dimer≥3.35mg/l (OR 7.85, 95% CI: 3.21-19.21, P=0.001)were associated with increased risk of 3-month mortality.Conclusions: AF-related AIS patients with concurrent high D-dimer and pneumonia increased risk of 3-month mortality and death/severe disability, plasma D-dimer may have predictive value in outcome after AF-related AIS with pneumonia.