Pulmonary embolism (PE) is one of the serious cardiopulmonary diseases that can endanger life. Early diagnosis and timely treatment are key factors to reduce its high mortality rate. Abdominal pain is not currently included in the symptoms of PE in textbooks and guidelines. A 49-year-old man was hospitalized for an exacerbation of right upper quadrant abdominal pain and sudden left upper quadrant pain that lasted for 2 hours. The patient was initially misdiagnosed as cholecystitis and pneumonia, and later was diagnosed as PE by computed tomography pulmonary angiography (CTPA). The patient received low molecular weight heparin for anticoagulant therapy. His abdominal pain disappeared after one week. The patient was later discharged. Sometimes abdominal pain may be the only manifestation of PE. However, most clinicians do not think of the possibility of PE in patients with abdominal pain. This might have contributed greatly to the rate of misdiagnosis of PE in the past. We hope to improve the alertness of the diagnosis of PE in clinical practice. In patients with abdominal pain, the possibility of PE should be considered to avoid mis- or under-diagnosis.