Identification of the pathophysiology associated with Eisenmenger syndrome has led to the evaluation of targeted therapies. Iloprost is one such targeted therapy used for patients with Eisenmenger syndrome. This study aimed to assess the efficacy and safety of iloprost used for patients with Eisenmenger syndrome. In this study, 12 patients with Eisenmenger syndrome (mean age, 33.2 ± 12.1 years; 75% female) started receiving iloprost 10 μg/dose administered six times a day. Of the 12 patients, 9 were classified as New York Heart Association (NYHA) functional class 3, and three were categorized as functional class 4. Changes in 6-min walk distance, NYHA functional class, oxygen saturation at resting, and results after the 6-min walk test were checked, as well as changes in right ventricle diameter and pulmonary arterial pressure shown by echocardiography. The distance during a 6-min walk increased from 255.8 ± 120.4 to 349.4 ± 134.7 m (p = 0.013), and 10 patients improved their NYHA functional class by one grade (p = 0.007). The mean resting oxygen saturation (SpO₂) increased from 80.6 ± 14.2 to 84.9 ± 13.0% (p = 0.040), and after the 6-min walk test, it increased from 63.8 ± 22.9 to 68.8 ± 21.5% (p = 0.007). The mean right ventricle diameter during the diastolic phase changed from 53.7 ± 4.8 to 51.4 ± 3.9 mm (p = 0.068), and the mean pulmonary arterial pressure changed from 62.8 ± 13.7 to 58.9 ± 11.7 mmHg (p = 0.059). Neither death nor critical adverse effects occurred for any patients. Mild headache and dyspnea were common reports during the iloprost treatments. No patients stopped the therapy due to these adverse effects. Iloprost is well tolerated and appears to be beneficial in the management of patients with Eisenmenger syndrome.