Reactivation of cytomegalovirus (CMV) leading to retinitis has been commonly reported in association with human immunodeficiency virus (HIV) infection or iatrogenic suppression of the immune system, including transplant recipients. Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy in the pediatric age group, and alveolar histology is associated with unfavorable outcome. Presently described is case of RMS with alveolar histology in a 12-year-old male who developed CMV bilateral retinitis during prolonged period of neutropenic fever after 40 weeks of chemotherapy. He was diagnosed based on CMV-DNA polymerase chain reaction in blood and urine samples, and responded well to intravenous gancyclovir treatment. A high index of suspicion for reactivation of CMV leading to retinitis should be maintained and, if needed, investigated, not only in patients with HIV infection or transplant recipients, but also all patients who are iatrogenically immunosuppressed, including those who experience prolonged neutropenic fever due to lengthy courses of radiotherapy and chemotherapy.