Background and Objectives: Primary amenorrhea (PA) is a clinical presentation of various underlying etiologies, including hormonal, genetic, and anatomical abnormalities. In Saudi Arabia, data on PA remain limited. This study aimed to characterize the etiologies, clinical features, diagnostic approaches, and management outcomes of PA in a Saudi population. Materials and Methods: This retrospective multicenter study reviewed medical records of females diagnosed with PA between July 2013 and July 2023 across tertiary and secondary care institutions. Data on clinical presentation, hormonal and imaging findings, genetic testing, and therapeutic interventions were collected and analyzed. Results: A total of 72 patients met the inclusion criteria. The mean age at diagnosis was 17.9 ± 4.72 years. The most prevalent etiology was hypergonadotropic hypogonadism (50%), followed by eugonadism with outflow tract abnormalities (20.8%) and hypogonadotropic hypogonadism (18.1%). Primary ovarian insufficiency (25%) and Turner syndrome (16.7%) were the leading specific diagnoses. Hormonal therapy, primarily conjugated estrogens, was the mainstay of treatment. Surgical intervention was indicated in 16.7% of cases. Follow-up showed significant improvement in Tanner staging for breast and pubic hair development (p = 0.0002 and p = 0.0033, respectively). Conclusions: Hypergonadotropic hypogonadism is the leading cause of PA in this study, with hormonal profiling and Tanner staging serving as valuable diagnostic tools. The findings highlight the importance of a systematic evaluation incorporating hormonal, clinical, and imaging assessments to guide timely and effective management. These results provide essential baseline data for refining diagnostic protocols and optimizing care for individuals with PA in the region.