Aims This study determined the optimal positive end‐expiratory pressure levels in infants in supine and prone positions under general anesthesia using electrical impedance tomography (EIT). Methods This prospective observational single‐centre study included infants scheduled for surgery in the prone position. An electrical impedance tomography sensor was applied after inducing general anesthesia. The optimal positive end‐expiratory pressure in the supine position was determined in a decremental trial based on EIT and compliance. Subsequently, the patient's position was changed to prone. Electrical impedance tomography parameters, including global inhomogeneity index, regional ventilation delay, opening pressure, the centre of ventilation, and pendelluft volume, were continuously obtained up to 1 h after prone positioning. The optimal positive end‐expiratory pressure in the prone position was similarly determined. Results Data from 30 infants were analyzed. The mean value of electrical impedance tomography‐based optimal positive end‐expiratory pressure in the prone position was significantly higher than that in the supine position 10.9 (1.6) cmH2O and 6.1 (0.9) cmH2O, respectively (p < .001). Significant differences were observed between electrical impedance tomography‐ and compliance‐based optimal positive end‐expiratory pressure. Peak and mean airway, plateau, and driving pressures increased 1 h after prone positioning compared with those in the supine position. In addition, the centre of ventilation for balance in ventilation between the ventral and dorsal regions improved. Conclusion The prone position required higher positive end‐expiratory pressure than the supine position in mechanically ventilated infants under general anesthesia. EIT is a promising tool to find the optimal positive end‐expiratory pressure, which needs to be individualized.