Mutations in seizure threshold 2 ( SZT2 ) gene on chromosome 1p34.2 are an of late identified cause of epilepsy and epileptic encephalopathy. We report a 3-year-old girl who presented with developmental delay, dysmorphic facies, refractory seizures, and subsequent developmental regression. Despite significant multifocal epileptiform abnormalities on her electroencephalogram, she had a paucity of generalized discharges indicating a functional deficiency of corpus callosum inspite of its increased thickness seen on magnetic resonance imaging. Her clinical exome sequencing revealed a homozygous single base pair duplication in the SZT2 gene that resulted in a frameshift mutation and premature truncation of the protein. Our case emphasizes the role of SZT2 gene in the diagnostic algorithm of early childhood refractory epilepsy especially in the context of a thick yet dysfunctional corpus callosum.