Controlling complex networks of nonlinear neurons is an important problem pertinent to various applications in engineering and natural sciences. While in recent years the control of neural populations with comprehensive biophysical models or simplified models, e.g., phase models, has seen notable advances, learning appropriate controls directly from data without any model assumptions remains a challenging and less developed area of research. In this paper, we address this problem by leveraging the network’s local dynamics to iteratively learn an appropriate control without constructing a global model of the system. The proposed technique can effectively regulate synchrony in a neuronal network using only one input and one noisy population-level output measurement. We provide a theoretical analysis of our approach and illustrate its robustness to system variations and its generalizability to accommodate various physical constraints, such as charge-balanced inputs.