Hantavirus infections and leptospirosis can have similar clinical and epidemiological features. We present here a case study of a young farmer with fever during the post-flood leptospirosis outbreak in Anuradhapura, Sri Lanka, in 2011. He presented with a classical clinical picture of leptospirosis and was managed and notified as a case of leptospirosis. Retrospective analysis of a stored serum sample confirmed acute hantavirus infection. Diagnosis of newly identified or emerging infectious diseases such as hantavirus infection is challenging due to the lack of diagnostic facilities in developing countries. This case highlights the need for improving diagnostic facilities, educating medical staff, and conducting population-based prospective studies on hantavirus infections in Sri Lanka.