Although pneumonia is associated with an increased risk of venous thromboembolism, patients with pulmonary embolism and concomitant pneumonia are uncommon. The aim of the present study was to investigate the clinical features of pulmonary embolism with coexisting pneumonia. We retrospectively compared clinical, radiologic and laboratory parameters between patients with pulmonary embolism and concomitant pneumonia (pneumonia group) and those with unprovoked pulmonary embolism (unprovoked group), and then between the pneumonia group and those with pulmonary infarction (infarction group). Of 794 patients with pulmonary embolism, 36 (5%) had coexisting pneumonia and six (1%) had no provoking factor other than pneumonia. Stroke was significantly more common in the pneumonia group, than either the unprovoked group or the infarction group. In the pneumonia group, fever was significantly more common and serum C-reactive protein levels were significantly higher. By contrast, central pulmonary embolism and right ventricular dilation on computed tomography were significantly less frequent in the pneumonia group. In addition, an adverse outcome due to pulmonary embolism was less common in the pneumonia group than in either of the other two groups. The coexistence of pulmonary embolism and pneumonia is rarely encountered in clinical practice, especially without the presence of other factors that could provoke venous thromboembolism and is commonly associated with stroke. It is characterized by lower incidences of central pulmonary embolism and right ventricular dilation and by a lower rate of adverse outcomes due to pulmonary embolism itself.