Hand, Foot, and Mouth Disease (HFMD) is a common viral illness primarily affecting young children and is characterized by its high contagiousness. This report presents a unique case of HFMD-related onychomadesis in a 5-year-old boy from Punjab, India, in September 2022. The patient initially exhibited typical HFMD symptoms, including a mild fever, oral ulcers, and skin lesions. However, eight days following the resolution of these symptoms, an unusual manifestation emerged: discolouration and roughness of the right index finger’s nail plate. Unlike conventional onychomadesis cases associated with HFMD, this presentation commenced at the distal edge of the nail, gradually extending in width to involve the entire free edge, with additional changes such as longitudinal striations and pitting. Subsequently, the subungual area became affected, with skin exfoliation and hyperkeratosis. Remarkably, the nail plate detached spontaneously, revealing a yellowish discoloured nail bed beneath. The affected nail eventually regrew to normalcy. This case highlights the importance of considering atypical onychomadesis as a potential complication of HFMD, challenging the conventional understanding of proximal nail separation in HFMD-related onychomadesis. The spontaneous resolution of symptoms without active intervention strongly suggests a link between HFMD and this nail disorder. Clinicians should be aware of such atypical presentations to ensure accurate diagnosis and management, especially in pediatric patients with a history of HFMD. Further research is needed to elucidate the underlying mechanisms of HFMD-related nail complications and to better guide clinical practice in similar cases.