Background: Persistent pulmonary hypertension is still an issue in newborn period with different treatment strategies. In this study, we aimed to evaluate the three-year experience of a neonatal intensive care unit on use of sildenafil citrate for treating newborns with persistent pulmonary hypertension. Methods: Twenty-nine newborn patients with the diagnosis of persistent pulmonary hypertension solely treated by sildenafil citrate (2 mg/kg per dose, orally, three times a day) in intensive care unit of a private hospital between 2018 and 2021 were retrospectively analyzed. Results: The newborns that underwent sildenafil treatment and the newborns that received no treatment had statistically similar length of hospital stay (p = 0.188). The premature newborns had significantly lower systolic and diastolic blood pressure than the term newborns on their first day of sildenafil treatment (p = 0.001 for both). The premature newborns had significantly lower systolic, diastolic, and right ventricular systolic pressure than the term newborns on their day of hospital discharge (p = 0.003, p = 0.013 and p = 0.001 respectively). The premature newborns had significantly lower systolic, diastolic, and right ventricular systolic pressure on their day of hospital discharge than their first day of sildenafil treatment (p = 0.039, p = 0.041 and p = 0.043 respectively). The term newborns had also significantly lower systolic, diastolic, and right ventricular systolic pressure on their day of hospital discharge than their first day of sildenafil treatment (p = 0.001 for each). Conclusions: Sildenafil citrate can be considered as an efficient and safe alternative for the treatment of persistent pulmonary hypertension in newborn at the in tertiary neonatal intensive care units without nitric oxide and devices.