The present invention relates to pharmaceutical compositions comprising a prostacyclin, a cationic compound, and a surfactant. Particulate compositions, including liposomal, solid nanoparticulate prostacyclin compositions, including treprostinil formulations comprising cationic compound and the surfactant are also described. The present invention also relates to a system comprising the pharmaceutical composition and an inhalation device. Methods for treating pulmonary hypertension and portopulmonary hypertension with the compositions and systems described herein are also provided.