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Neonatal cyanosis is commonplace, usually from respiratory or cardiac causes. Consideration of alternative or combined aetiologies was required when a 3-hour-old term male neonate with central cyanosis, low oxygen saturation (SpO2), and persistent pulmonary hypertension of the newborn (PPHN) confirmed on echocardiography, failed to respond to PPHN interventions. The high oxygen saturation gap and methemoglobin (MetHb) level of 16.2% shifted the working diagnosis to methemoglobinaemia. Possible triggering drugs were stopped and methylene blue was given without effect, prompting testing for haemoglobin variants. Though the SpO2 remained in the mid-80s, MetHb levels decreased, pulmonary pressures normalised by day of life (DOL) 4, and he was discharged home on DOL 22. Diagnostic testing confirmed the haemoglobin F-M-Fort Ripley mutation (HBG2: c.277C>T), a variant that affects fetal haemoglobin only and is therefore self-limited. In this case, the concurrent presentation of PPHN and congenital methaemoglobinaemia created significant diagnostic and therapeutic challenges.