Cutting-edge methodologies and techniques are required to understand complex neuronal dynamics and pathological mechanisms. Among them, optical tools stand out due to their combination of non-invasiveness, speed, and precision. Examples include optical microscopy, capable of characterizing extended neuronal populations in small vertebrates at high spatiotemporal resolution, or all-optical electrophysiology and optogenetics, suitable for direct control of neuronal activity. However, these approaches necessitate progressively higher levels of accuracy, efficiency, and flexibility of illumination for observing fast entangled neuronal events at a millisecond time-scale over large brain regions. A promising solution is the use of acousto-optic deflectors (AODs). Based on exploiting the acousto-optic effects, AODs are high-performance devices that enable rapid and precise light deflection, up to MHz rates. Such high-speed control of light enables unique features, including random-access scanning or parallelized multi-beam illumination. Here, we survey the main applications of AODs in neuroscience, from fluorescence imaging to optogenetics. We also review the theory and physical mechanisms of these devices and describe the main configurations developed to accomplish flexible illumination strategies for a better understanding of brain function.