Background Given the improved convenience of oral prostacyclins, there is a shift toward their use in treating pulmonary arterial hypertension (PAH). Objectives Our objective was to compare patient characteristics, medication adherence, healthcare resource use (HCRU), and costs among patients receiving oral treprostinil or selexipag. Methods We used Truven Health MarketScan Commercial and Medicare databases to identify patients with PAH with a diagnosis code for pulmonary hypertension (PH) plus a prescription for oral treprostinil or selexipag from July 2013 to September 2017. Medication adherence, persistence, and all-cause and PAH-related HCRU and costs were compared between cohorts during the 6-month follow-up. Adjusted healthcare costs were obtained using recycled predictions and bootstrapped samples. Results A total of 256 (130 oral treprostinil, 126 selexipag) patients fulfilled the study criteria. The oral treprostinil cohort was more likely to be male, to have previously used parenteral prostacyclins, and to have higher outpatient costs at baseline than the selexipag cohort. During follow-up, both cohorts had similar proportions of patients who were adherent to and persistent with their respective therapies. All-cause and PAH-related medical utilization was generally similar between cohorts. The oral treprostinil cohort had 66.9% lower total PAH-related healthcare costs (mean difference − $75,183; 95% confidence interval [CI] − 102,584 to − 49,771) and 70.6% lower PAH-related pharmacy costs (mean difference − $76,439; 95% CI − 104,512 to − 51,458) than the selexipag cohort, with similar differences in all-cause healthcare and pharmacy costs. Conclusions Lower all-cause and PAH-related total healthcare and pharmacy costs were observed in patients receiving oral treprostinil compared with those receiving selexipag. It will be important to study longer-term costs and clinical outcomes.