Kleefstra syndrome is a genetic disorder that may involve different parts of the body, but its main characteristics are intellectual disability and childhood hypotonia. We report a 10-year-old mentally retarded male patient who presented with seizure. His medical history revealed recurrent upper respiratory infections, neurodevelopmental delay, and epilepsy. It was also found that he had had a hospitalization in the neonatal intensive care unit for five days due to tachypnea, low APGAR score, and meconium aspiration syndrome. His brain MRI had shown some degree of distension of the lateral cerebral ventricles with the basal cistern. The electromyography and the nerve conduction velocity were however normal. He was diagnosed with Kleefstra syndrome by the loss of the EHMT1 gene. He is now under treatment by piracetam and work-therapy. This is the second case report of this syndrome in Iran. This case presentation aims to improve the diagnosis of Kleefstra syndrome patients, as a rare syndrome with non-characteristic manifestations.