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Cardiac myxomas are the most common primary benign cardiac tumors and typically present with obstructive or embolic cardiac symptoms. However, fever of unknown origin (FUO) is a rare and under-recognized presentation that may lead to diagnostic delays, particularly in regions endemic for infectious diseases. We report the case of a 24-year-old male from a tropical region of the country who presented with persistent high-grade fever associated with chills and rigors. The clinical picture initially suggested a vector-borne illness such as malaria or kala-azar, both endemic in his region. The malarial antigen test was positive with a negative smear test. Despite empirical antimalarial therapy, the fever persisted. The patient also had a mid-diastolic murmur at the left lower sternal border, which prompted early echocardiographic screening. A large right atrial myxoma was identified; surgical resection of the tumor was performed, and microbiological evaluation of the resected tissue was negative for any pathogen, and histopathology confirmed atrial myxoma. Postoperatively, the patient made a full recovery with complete resolution of fever. This case underscores the importance of considering cardiac myxoma in the differential diagnosis of FUO, especially when conventional infectious causes are excluded. In regions with high prevalence of tropical infections, such presentations may be easily misattributed, leading to diagnostic delays. Routine echocardiographic evaluation should be considered in patients with FUO and atypical or unexplained cardiopulmonary symptoms to facilitate early diagnosis and curative surgical intervention.