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Background The aim of this prospective, randomized trial was to compare analgesia, sedation, and cardiorespiratory function in children after thoracoscopic surgery for pectus excavatum repair, using two types of analgesia—epidural block with bupivacaine plus fentanyl vs patient-controlled analgesia (PCA) with fentanyl. Methods Twenty-eight patients scheduled for thoracoscopic pectus excavatum surgery were randomly assigned to receive either thoracic epidural block or i.v. PCA for postoperative analgesia. Pain was assessed using a visual-analogue scale (VAS). The Ramsay sedation score, arterial pressure, ventilatory frequency, and heart rate were also measured, and blood gas analysis was performed regularly during the first 48 h after surgery. Results A significant decrease in the VAS pain score, Ramsay sedation score, heart rate ventilatory frequency, systolic and diastolic blood pressure, and Pa co 2, and a significant increase in Pa o 2 and oxygen saturation were found over time. Patients in the PCA group had significantly higher Pa co 2 values. In addition, a significantly slower decline of systolic blood pressure and heart rate, and faster recovery of Pa co 2 were found in PCA patients than in patients with epidural block. Conclusions I.V. fentanyl PCA is as effective as thoracic epidural for postoperative analgesia in children after thoracoscopic pectus excavatum repair. Bearing in mind the possible complications of epidural catheterization in children, the use of fentanyl PCA is recommended.