Objective To explore the risk factors of pulmonary embolism (PE) in the patients initially diagnosed as neurointensive care unit hospital-acquired pneumonia (NICUHAP) with increased D-dimer level. Methods A case-control study was taken to observe the clinical data from the patients with NICUHAP who were initially diagnosed in the Tenth People's Hospital of Tongji University between Jan. 2007 and Jan.2018. According to the results of computed tomography pulmonary angiography (CTPA) examination, the patients were divided into PE group and non-PE group. The pulmonary artery occlusion index (PAOI) was calculated in the patients of the PE group. Univariate and multivariate logistic regression analyses were performed to explore the risk factors for PE. Results A total of 129 patients initially diagnosed as NICUHAP were included in this study and received CTPA examination. The median D-dimer levels of PE patients (n=75) and non-PE patients (n=54) were 3.97 mg/L and 0.88 mg/L, respectively, and the difference was significant (P<0.05). The PAOIs of 70 (93.3%) PE patients were below 30%. There was no significant correlation between the D-dimer level and PAOI. Age, coronary heart disease, chronic obstructive pulmonary disease, varicose veins of lower limbs, thoracodynia, shortness of breath, hemoptysis, chest tightness, fever (body temperature>38.5℃), and elevated cardiac troponin I level were possible independent risk factors for PE. Conclusion The patients initially diagnosed as NICUHAP with PE have elevated D-dimer level compared with the patients without PE. There is no significant correlation between D-dimer level and PAOI. The patients initially diagnosed as NICUHAP, who are older than 60 years, or accompanied with coronary heart disease, chronic obstructive pulmonary disease, varicose veins of lower limbs, thoracodynia, shortness of breath, hemoptysis, elevated cardiac troponin I level or with a body temperature below 38.5℃, need CTPA examination to exclude PE.