Background Though simple febrile seizures do not cause significant and lasting neurological deficits, complex febrile seizures (CFS) can result in neurologic sequelae. Because CFS causes cortical focal injuries and other brain lesions, it needs to be evaluated. Objective The objective of this study was to evaluate the MRI brain changes in CFS, the incidence of seizures in children aged six months to five years, and their severity in relation to MRI findings of the brain. Methods In this observational study, 36 children aged six months to five years, having fever with seizure, and fulfilling the criteria of CFS were enrolled within 48 hours of the episode. Detailed clinical and neurological examinations were performed with MRI scans to find out the probable CNS lesions of CFS. Two radiologists separately evaluated all MRI brains. Results MRI lesions of the brain were found in 11 (30.56%) CFS patients. Generalized tonic-clonic seizures (GTCS) (n=31, 86.11%) were the most common type of seizure among CFS cases. Cortical focal hyperintensity (CFH) (42.1%) was the most common MRI presentation. Positive MRI findings were significantly associated with focal convulsions (n=5, 100%) as compared to GTCS cases (n=6, 19%) (p=0.001). Conclusions CFH is the most common abnormality in the MRI brain among CFS cases. CFS patients with focal seizures or prolonged seizures in 24 hours have higher abnormal neuroimaging findings. MRI should be considered a preferred investigatory tool for detecting CNS pathology in CFS cases. Follow-up studies are needed to determine the long-term outcomes of CNS lesions in children with CFS.