Purpose Optimal management of the bone flap after craniotomy for intracranial infection has not been well defined in the pediatric population. This study reviewed the outcomes of a single Canadian center where immediate replacement of the bone flap was standard practice. Methods This is a retrospective study of all patients who underwent craniotomies for evacuation of epidural or subdural empyema at a single center from 1982 to 2018. Patients were identified using the prospective surgical database maintained by the Division of Pediatric Neurosurgery at BC Children's Hospital. Primary outcome was treatment failure, defined as reoperation at the site of initial surgery for removal of an infected bone flap or repeat drainage of empyema under the replaced bone flap. Secondary outcome was any reoperation for recurrent infection at any site. Results Twenty-four patients met the inclusion criteria with a minimum of 3-month follow-up from the index intervention. Treatment failure occurred in four patients (17%), all of whom required repeat surgery for further drainage of pus underlying the bone flap. Mean time to repeat surgery was 13 days. Any reoperation for recurrent infection at any site occurred in three patients. Seven out of 24 patients required a second surgery to evacuate empyema (29.2%). Age, sex, epidural or subdural location, osteomyelitis, and bone flap wash were not associated with the primary outcome of treatment failure. Conclusion Immediate replacement of the bone flap in the surgical management of pediatric subdural or epidural empyema is reasonable. Replacing the flap at the time of first surgery avoids the morbidity and costs of a subsequent reconstructive operation.