Pulmonary arterial hypertension (PAH) is a lethal, progressive disease with a complex pathogenesis. Bosentan, a dual endothelin receptor antagonist, and sildenafil, a phosphodiesterase type 5 inhibitor, are used to treat PAH. In this study, we aimed to develop a liquid chromatography-tandem mass spectrometry method (LC–MS/MS) to measure the levels of bosentan, sildenafil, and their active metabolites in patients with PAH. We have developed an LC–MS/MS measurement procedure using a liquid–liquid extraction to measure serum drug concentrations and validated the procedure according to Clinical and Laboratory Standards Institute (CLSI) protocols. Finally, the validated method was used to measure the levels of sildenafil, bosentan, and their metabolite in pediatric PAH patients. The method was linear in the range of 0.975–1000 ng/ml and 0.76–3125 ng/ml for sildenafil and bosentan, respectively. LOQ values of sildenafil and bosentan were determined as 1.95 and 1.50 ng/ml, respectively. A method for measuring the levels of sildenafil and bosentan was developed that is rapid, robust, inexpensive, and requires a small serum volume. In addition, the validated method measured these drugs’ levels and metabolites in pediatric patients with PAH. The results show that the established method can routinely monitor drug levels.