The human brain is the least accessible of all organs and attempts to study it in vivo rely predominantly on neuroimaging. Functional near-infrared spectroscopy (fNIRS) allows for the study of cortical neural activity in a non-invasive manner that may resemble free-living conditions. Moreover, compared to other neuroimaging tools, fNIRS is less expensive, it does not require the use of ionizing radiation, and can be applied to all study populations (patients suffering from claustrophobia, or neonates). In this narrative review, we provide an overview of the available research performed using fNIRS in patients with diabetes and obesity. The few studies conducted to date have presented controversial results regarding patients with diabetes, some reporting a greater hemodynamic response and others reporting a reduced hemodynamic response compared to the controls, with an unclear distinction between types 1 and 2. Subjects with obesity or a binge eating disorder have reduced prefrontal activation in response to inhibitory food or non-food stimuli; however, following an intervention, such as cognitive treatment, prefrontal activation is restored. Moreover, we discuss the potential of future applications of fNIRS for a better understanding of cortical neural activity in the context of metabolic disorders.