Pachydermodactyly, an uncommon variant of digital fibromatosis, predominantly affects young men and results in fibrous swelling on the sides of the proximal interphalangeal joints. It is generally considered benign and asymptomatic, requiring only regular follow-up. Nevertheless, the absence of established diagnostic criteria has led to misdiagnoses, prompting the administration of unnecessary medications. In this report, we present a 14-year-old Japanese male with symptomatic pachydermodactyly, necessitating careful differentiation from juvenile idiopathic arthritis (JIA) due to the presence of morning stiffness. Despite exhibiting typical pachydermodactyly features, the patient’s age and symptoms suggested rheumatoid factor-negative polyarticular JIA. However, the lack of inflammatory findings precluded a JIA diagnosis. Following confirmation of the absence of uveitis and progression of bone destruction, the morning stiffness spontaneously resolved without active treatment. However, the patient underwent surgery for aesthetic reasons to alleviate the persistent swelling. Our case highlights the nuances of symptomatic pachydermodactyly, with a literature review revealing similarities between symptomatic and asymptomatic cases. This challenges the suitability of asymptomatic status as a definitive diagnostic criterion. Our findings contribute to the ongoing efforts in establishing diagnostic criteria for pachydermodactyly, aiming to reduce misdiagnoses and unnecessary medications in patients.