Control mechanisms for the rhythms of neuronal ensembles based on the neuromodulation effect are described and implemented. The biological mechanisms of neuromodulation are briefly outlined, and some aspects are highlighted to control the activity patterns of interconnected neurons forming ensembles. Within the suggested model, neuromodulation is a change in the neuron’s properties responsible for its sensitivity to excitatory and inhibitory impacts (and, therefore, for its activity). This change is initiated by certain neurotransmitters (modulators), which indirectly influence the electrical activity of all neurons sensitive to them. The discrete asynchronous chemical interaction model of biological neurons in small neural networks is modified and extended to implement this control mechanism inherent in living organisms. The key effect of neuromodulation is the rapid functional reorganization of neural networks without changing their structural properties. Activity patterns are changed not via costly changes in the connections between neurons but by changing the chemical environment of the ensemble’s neurons. The mechanism of neuromodulation is formalized. The new model is implemented in software, and several computational experiments are performed to change the gait of hexapods.