The aim of this study was to investigate the correlation between circulating endothelial progenitor cell (EPC) levels and plasma prostacyclin (PGI2) concentrations in pulmonary hypertension (PH) rat models. Monocrotaline was used to induce PH, and the number of CD34/Flk-1-double-positive mononuclear cells in peripheral CD45-negative blood was counted by flow cytometry, which reflected EPC circulation. The Greiss method was used to detect the plasma PGI2 concentration. Simple linear regression analysis was used to analyze the relationship between EPC and PGI2. Furthermore, the expressions of cycled EPC, CD34, and Flk-1 were detected under in vitro culture conditions. The mean circulating EPC level in the PH model group (0.013 ± 0.004%) was significantly lower (P < 0.01) than that in the control group (0.036 ± 0.009%). The concentration of plasma PGI2 also significantly decreased (24.36 ± 2.08 vs 58.34 ± 3.31 μM; P < 0.01). There was a positive correlation between EPC and PGI2 (r = 0.870, P < 0.05). Under in vitro culture conditions, the EPC number and the CD34 and Flk-1 expression levels in the PH model group were significantly lower than those in the control group. Together, these results suggest that the occurrence of PH may be associated with decreased plasma PGI2 concentrations, resulting in the reduction of circulating EPC.