Methaemoglobinaemia is a potentially life-threatening condition characterised by hypoxaemia, cyanosis, pallor, fatigue, metabolic acidosis, headache and in severe cases, coma or death. Topical anaesthetics have been reported to cause methaemoglobinaemia. Topical benzocaine was specifically implicated in roughly 66% of anesthetic-induced methaemoglobinaemia cases in a large systematic review in adults. This complication has occurred often in adult patients with pre-existing comorbidities resulting in diminished use in children overall with only few paediatric cases reported worldwide. Additionally, there is growing evidence of a link between sepsis and methaemoglobinaemia due to increased circulating nitrous oxide from infectious pathogen metabolism. In this report, we discuss a case of a 16-year-old young boy, being evaluated for suspected endocarditis, presenting with acute methaemoglobinaemia after use of topical benzocaine spray for transesophageal echocardiogram. This case exemplifies the importance of blood gas with co-oximetry testing in all cases of refractory hypoxemia who have had procedures requiring topical anaesthetics.