Systemic lupus erythematosus (SLE) often presents with cytopenia(s); however, pancytopenia is found less commonly, requiring the consideration of possible aetiologies other than the primary disease. The authors describe the case of a female patient with a recent diagnosis of SLE admitted through the Emergency Department with fever of unknown origin and severe pancytopenia. She was medicated with prednisolone, hydroxychloroquine, azathioprine, amlodipine and sildenafil. Extensive investigation suggested azathioprine-induced myelotoxicity. However, the patient was found to have a concomitant cytomegalovirus (CMV) infection, with oral lesions, positive CMV viral load as well as the previously described haematological findings. Pancytopenia is always a diagnostic challenge, with drug-induced myelotoxicity, especially secondary to azathioprine, being a rare aetiology. This report reiterates the importance of the differential diagnosis of pancytopenia, especially in immunosuppressed patients with increased risk for opportunistic infections.