Background: Circumcision, the surgical removal of the prepuce, remains one of the most debated procedures worldwide. While it is advocated for its potential role in reducing sexually transmitted and urinary tract infections, it continues to be primarily driven by sociocultural and religious factors. The prepuce, however, is a specialised tissue with protective, sensory, and reconstructive functions, and its routine removal raises anatomical and ethical concerns. Objectives: To evaluate the histological features of the neonatal prepuce excised during circumcision and also to assess its functional and surgical significance. Methodology: A prospective observational study was conducted between September and November 2024 at Immaculate Heart of Mary Specialist Hospital Nkpor, Anambra State, Nigeria. Thirty-six neonates undergoing circumcision by Plastibell or freehand method were recruited following informed parental consent. Excised prepuces were formalin-fixed, processed, stained with haematoxylin and eosin, and examined for epithelial structure, layer thickness, vascularity, and neural distribution. Data were analysed descriptively using SPSS. Results: Participants had a mean age of 14.6 ± 6.7 days and a mean weight of 3.6 ± 0.7 kg. Histology revealed five distinct layers: epidermis, dermis, Dartos fascia, lamina propria, and mucosa, with a mean thickness of 3.96 ± 0.95 mm. The lamina propria was highly vascularised (5–9 vessels/mm²), and nerve bundles were present in 86% of Dartos samples. Both epidermis and mucosa showed keratinised squamous epithelium with intact basement membranes. Inflammatory infiltrates were seen in 44% of specimens, but no dysplasia or malignancy was observed. Conclusion: The neonatal prepuce is a complex tissue with structural and functional importance. Routine circumcision lacks sufficient histological justification, warranting multidisciplinary review and public debate on its continued practice.