An imperforate hymen (IH) is an uncommon congenital condition resulting from the failure of the synovaginal bulbus to canalize during embryonic development. While it typically presents with primary amenorrhea, cyclic pain, and hematocolpos, certain cases may exhibit unusual symptoms like constipation and obstructive uropathic disorders, which can often result in a delayed diagnosis. A 12-year-old female adolescent was observed with a history of progressively worsening cyclic abdominal pain, along with severe constipation and mild urinary disturbances. The physical examination revealed a suprapubic mass, as well as a hymen that entirely obstructed the vaginal introitus, showing a bluish protrusion. Initially, the patient received a diagnosis of vaginal agenesis; however, further examination revealed the presence of hematocolpometra linked to IH. The patient received a hymenectomy, resulting in symptomatic improvement and full resolution of the hematocolpos. The infrequency and clinical diversity of IH highlight the critical need for early detection via genital examination from birth, particularly to prevent misdiagnosis that could postpone treatment. Imaging techniques like ultrasound are crucial for distinguishing IH from related conditions, including vaginal agenesis. Additional investigations are essential to enhance clinical understanding and guarantee effective management for individuals affected by this condition.