The diagnosis of pulmonary embolism (PE) needs clinical manifestations and radiological findings. CT angiography (CTA) of pulmonary vessels is the gold standard of diagnosis of PE. However, endobronchial ultrasound (EBUS) can be a reliable and accurate alternative method of diagnosis in patients who are not candidates for CTA. Invasiveness and high cost are still the major limitations for EBUS, however, they should be considered in the appropriate population in future practice. We present a case of a 62-year-old asymptomatic male diagnosed with PE during EBUS for mediastinal lymph node assessment and biopsy.