Hypertrophic osteoarthropathy (HOA), also known as pachydermoperiostosis is an unusual cause of digital clubbing. It is a rare osteo-arthro-dermopathic syndrome which is associated with clubbing of fingers, thickening of skin in the face and scalp, seborrhea, and subperiosteal new bone genesis. It is divided into two types: Primary (PHOA) and secondary HOA, with the latter being common. PHOA accounts for a very meager portion of HOA cases. PHOA is usually inherited in an autosomal dominant fashion and rarely follows autosomal recessive inheritance pattern. We report a case of a male who presented with a history of progressive and painful enlargement of distal phalanges of hands and feet for 6 years. After all examinations and tests ruled out the secondary causes for HOA, genetic sequencing was performed to confirm the diagnosis of PHOA. Sequencing revealed homozygous nonsense mutation in SLCO2A1 gene. This mutation is postulated to impair the degradation of prostaglandin E2 (PGE2), leading to its elevated levels. PHOA is an atypical cause of clubbing which usually poses a challenge in diagnosis. This report also underscores the importance of genetic sequencing in appropriate diagnosis and management of the PHOA.