Micropenis is a rare congenital condition characterized by a stretched penile length more than 2.5 standard deviations below the mean for age and sex. This report discusses a rare case of micropenis in a newborn male, detailing the clinical evaluation, diagnosis, and comprehensive management strategies. The patient presented with an abnormally small penis at birth, confirmed through clinical measurements, hormonal assessments, and genetic testing. The management involved initiating endocrine therapy and careful monitoring to address potential underlying causes and associated conditions. This case underscores the importance of early diagnosis and a multidisciplinary approach for optimal outcomes in patients with micropenis.