Pachydermoperiostosis (PDP) is a rare disorder characterized by pachydermia, digital clubbing, periostitis, and an excess of affected males. It is the primary form of hypertrophic osteoarthropathy (HOA) and there are some rare associations of PDP with other disorders. Here we describe a patient with Crohn’s disease associated with PDP. A 26-year-old man, who was a known case of Crohn’s disease, referred with diffuse swelling in the upper and lower limbs and cutis verticis gyrata since 7 years ago. PDP was suspected and endocrinological and radiological studies were conducted for the evaluation of underlying disease. He was prescribed celecoxib, low-dose prednisolone, and pamidronate to control the swelling, periostitis, azathiopurine, and mesalazine according to gastrointestinal involvement. In conclusion, it is important to identify this condition since a misdiagnosis might subject the patient to unnecessary investigations.