The purpose of this study was to investigate the influence of 3-T intraoperative MRI (ioMRI) on the extent of resection of pediatric focal epileptogenic lesions, residual lesion volumes, and postoperative seizure outcomes. All surgical procedures for focal epilepsy from 2003 to 2017 were retrospectively reviewed. Patients were divided into two groups: those who underwent ioMRI and those who did not. Each group was subdivided into two subcategories according to preoperative MRI visualization of the lesion: those with well-defined and those with poorly defined lesions. The volumes of preoperative lesions and postoperative residual lesions were delineated. Outcome data and patient characteristics were reviewed. The results were compared between the two groups and the two subcategories. Eighty patients were included: 45 in the ioMRI group (24 with well-defined lesions, 21 with poorly defined lesions) and 35 in the non-ioMRI group (18 with well-defined lesions, 17 with poorly defined lesions). The well-defined lesions included tumors and vascular lesions. The poorly defined lesions included malformations of cortical development, hippocampal sclerosis, and tuberous sclerosis. The mean follow-up duration was 5.1 ± 3.3 years. The rate of gross total resection was not significantly different between the ioMRI and non-ioMRI groups ( 0.46). However, ioMRI findings facilitated further resection during surgery, increasing gross total resection by an additional 11.1%. The ioMRI group had a significant reduction in percentage of residual volume ( < 0.001). Outcome data suggested that ioMRI is protective against poor Engel score ( = 0.048). Although ioMRI prolonged the mean operative time by 1.2 hours ( = 0.002), the additional time was not associated with additional complications. Integration of ioMRI into focal epilepsy surgery was associated with smaller residual lesions and was protective against poor Engel score. It prolonged the operative time but without increasing the number of complications.