Elizabethkingia anophelis, a gram-negative bacillus belonging to the Flavobacteriaceae family, is found in various environmental sources and has been associated with community and hospital outbreaks. Correct identification is crucial, guided by advanced genomic techniques, i.e., matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system with an updated database. The case fatality rate, ranging from 24 to 60%, underscores the need for timely recognition and appropriate management. Additionally, Elizabethkingia presents a challenge due to its recent discovery, misidentification history, and drug resistance. Here, we present a case of fatal infection in a 30-year-old male, who presented with pneumonia. It gradually progressed and ultimately proved fatal underscoring the virulence of the pathogen involved. It was a diagnostic challenge as it likely is the first reported instance of Elizabethkingia anophelis infection from Nepal.