Swyer syndrome (SS), or 46, XY pure gonadal dysgenesis, is a rare disorder of sex development. It typically presents with primary amenorrhea and an absence of secondary sexual characteristics. However, in rare cases, patients may exhibit atypical features such as spontaneous breast development and menstruation. This report details the case of a 13.5-year-old female with a 46, XY karyotype, fully developed secondary sexual characteristics, and unilateral gonadoblastoma. The primary clinical symptoms included generalized hirsutism and secondary amenorrhea, occurring ten months after experiencing two menstrual periods. Physical examination revealed a phenotypic female of normal height with apparently normal external genitalia but clitoromegaly. Breast and pubic hair development were at Tanner stage five. Noteworthy features included generalized hirsutism and a deep voice. Initial laboratory investigations showed follicle-stimulating hormone (FSH) at 0.39 mIU/mL, luteinizing hormone (LH) at 0.43 mIU/mL, testosterone at 1.96 ng/mL, and estradiol at 79.54 pg/mL. An abdominal computed tomography (CT) scan detected a 12 × 10 × 10.5 cm calcified mass on the left side of the pelvis, originating from the ovaries. Surgical excision of the mass, along with a left salpingo-oophorectomy, was performed. Histopathology confirmed the mass as a gonadoblastoma. Chromosomal analysis confirmed the diagnosis of XY pure gonadal dysgenesis (Swyer syndrome). This case highlights the importance of comprehensive genetic testing in females presenting with amenorrhea despite fully developed secondary sexual characteristics.