Rhabdomyosarcomas are neoplasms with a high degree of malignancy and arise from the embryonic mesenchyme. They represent approximately 5% of all pediatric tumors and their main locations are the head and neck (45%), trunk (40%), and extremities (15%). Twenty-five percent to 30% of the head and neck rhabdomyosarcomas appear in the orbit; however, its origin from the conjunctiva is rare, with few case reports published in the literature. We present the case of a five-year-old girl with a diagnosis of primary embryonic rhabdomyosarcoma of the conjunctiva, treated with surgery and chemotherapy. After completing the treatment, it was followed up with controls for oncological ophthalmology, pediatric hematology-oncology, and radiotherapy oncology every six months with magnetic resonance of the orbits. Two years after the end of treatment, the patient is disease-free. Conjunctiva rhabdomyosarcoma is a rare lesion, with few previously reported cases. In the reported case, the histopathological findings and positivity of the different immunohistochemical markers allowed a definitive diagnosis of rhabdomyosarcoma. The excellent prognosis of this pathology is probably linked to the early diagnosis of the disease and the timely administration of radical treatment. It is essential to be able to identify conjunctival rhabdomyosarcoma from its clinical and histopathological characteristics in order to achieve early diagnosis and provide adequate treatment to patients.