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Refractory gout and Lyme disease are distinct conditions that, when coexisting, pose significant diagnostic and therapeutic challenges, particularly in regions endemic for Lyme disease. This case report presents a 49-year-old male with a three-year history of gout, presenting with acute arthritis of the first metatarsophalangeal joint, unresponsive to standard urate-lowering therapy. Despite treatment with colchicine and prednisone, the patient’s symptoms persisted, and inflammatory markers remained elevated. Imaging revealed findings consistent with gouty arthritis, but due to the atypical treatment response, further testing was conducted. Serological analysis confirmed infection with Borrelia burgdorferi, establishing the diagnosis of concurrent Lyme disease. The addition of doxycycline to the treatment regimen resulted in significant clinical improvement within days. This case highlights the importance of considering Lyme disease in patients with refractory gout in areas endemic for Lyme disease. While rare cases of Lyme disease mimicking gout have been reported, this is among the first documented instances of their coexistence. Early recognition and appropriate antibiotic treatment are critical in preventing complications and ensuring optimal management of both conditions.