We used near-infrared spectroscopy (NIRS) to examine differences in neonates' orbito-frontal cortical activation in response to the odours of maternal breast milk and formula milk in terms of changes in the oxygenation of cerebral blood flow. Twenty-six healthy neonates were tested in their cribs while they slept in a silent room. The neonates were exposed to each olfactory stimulus by an experimenter. NIRS monitoring was performed using optodes placed above the bilateral anterior orbito-frontal gyri. The differences in oxygenated haemoglobin (oxy-Hb) values between baseline and stimulation were defined as the change in oxy-Hb. The degrees of change were calculated by an analysis of variance (ANOVA). A 2 (stimulus: breast milk and formula milk) × 2 (probe location: right and left) ANOVA showed that the odour of maternal breast milk (right/left: M = 0.28/0.48) induced a significantly (F = 6.36, p < 0.05) greater increase in the oxygenated blood of the orbito-frontal region than did the odour of formula milk (right/left: M = −0.03/−0.07). Differences in the intensity of odour had no significant influence on the blood oxygenation of the orbito-frontal region. Maternal breast milk odour increased oxygenated blood flow in the orbito-frontal region to a greater extent than did formula milk odour. These results suggest that neonates can distinguish between the odours of maternal breast milk versus formula.