The incidence of pediatric venous thromboembolism (VTE) has been increasing in the past few decades and can be associated with significant mortality and morbidity. There are known risk factors associated with VTE, including estrogen therapy. However, the relationship between testosterone and VTE remains unclear. Here, we present a 17-year-old female-to-male transgender patient without a history of inherited thrombophilia, who developed pulmonary embolism while receiving testosterone injections for gender dysphoria. Despite the limited data on testosterone and the risk of VTE, health care providers should counsel patients and family about the possible increased risk of VTE when starting testosterone.