Brain–gut axis represents a complex reflex circuit that integrates the communication between cortex and the digestive system. Disturbances of the neuromodulatory processes in the brain–gut axis generate functional digestive disorders mainly centered on the pain symptoms and motility disorders. This article reviews structural and pathophysiologic aspects of the brain–gut axis and explains how the neuromodulatory interventions currently used in order to treat gastrointestinal conditions related to the brain–gut axis disturbances. The neuromodulation can be realized by pharmacologic targeting mainly receptors in the periphery or using electrical stimulation applied at different levels of the nervous system or directly in the muscular layers of the bowels resulting in modulation of the digestive system activity. The efficacy of the methods using electrostimulation is dependent on the parameters of the physical system used: amplitude, frequency, burst time of the electrical current, and also the positioning of the electrodes. While pharmacologic interventions are largely used at the moment, neuromodulatory interventions involving electrical stimulation showed clinical efficacy in research trials and have promise.