Congenital methemoglobinemia is a rare condition caused by cytochrome b5 reductase deficiency, cytochrome b5 deficiency, or hemoglobin M disease. Newborn pulse oximetry screening was developed for the early detection of critical congenital heart disease; however, it also enables the early identification of other hypoxemic conditions. We present the case of a term neonate who was admitted to the neonatal unit after a failed pulse oximetry screening at 3 hours of age. Oxygen saturations remained between 89% and 92% despite an increase in oxygen therapy. Chest radiograph and echocardiogram results were normal. A capillary blood gas test had normal results except for a raised methemoglobin level of 16%. Improvement was seen on the administration of methylene blue, which also resulted in an increase in oxygen saturations to within normal limits. Further investigation revealed evidence of type I hereditary cytochrome b5 reductase deficiency as a result of a CYB5R3 gene mutation with 2 pathogenic variants involving guanine-to-adenine substitutions. Although mild cyanosis is generally the only symptom of type I disease, patients may later develop associated symptoms, such as fatigue and shortness of breath. If an early diagnosis is missed, these patients are likely to present later with a diagnostic conundrum and be subject to extensive investigation. This case represents the success of pulse oximetry screening in the early identification of subclinical hypoxemia in this infant. After the exclusion of other pathologies, a routine investigation of capillary blood gas provided the information that led to a diagnosis, which allowed for early and effective management.