Epilepsy is common in children with autism spectrum disorder (ASD) but little is known about how seizures impact the autism phenotype. The association between epilepsy and autism symptoms and associated maladaptive behaviors was examined in 2,645 children with ASD, of whom 139 had epilepsy, from the Simons Simplex Collection. Children with ASD and epilepsy had significantly more autism symptoms and maladaptive behaviors than children without epilepsy. However, after adjusting for IQ, only hyperactivity symptoms remained significantly increased (13% higher) in the epilepsy group. Among children with ASD without co-occurring intellectual disability, children with epilepsy had significantly more irritability (20% higher) and hyperactivity (24% higher) symptoms. This is the largest study to date comparing the autism phenotype in children with ASD with and without epilepsy. Children with ASD and epilepsy showed greater impairment than children without epilepsy, which was mostly explained by the lower IQ of the epilepsy group. These findings have important clinical implications for patients with ASD.