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This case report highlights the diagnostic limitations of nasopharyngeal swabs in diagnosing COVID-19. This patient had a positive travel history, typical symptoms (fever, dry cough, dyspnea) and two negative nasopharyngeal swabs (NPS). He deteriorated clinically and required intubation. After intubation, bronchoalveolar lavage was used to sample the lower respiratory tract, which confirmed the diagnosis of COVID-19. This case demonstrates the diagnostic limitation of relying solely on nasopharyngeal swab PCR for the diagnosis of COVID-19. NPS tests may result in false negatives with incorrect sampling technique or if the sampling is done while upper tract viral load is low, such as very early or late during the illness course. During this pandemic, we posit that clinicians should maintain a high degree of suspicion based on supportive clinical findings despite negative PCR testing as this has implications for hospital infection control procedures.