•  In order to understand the underlying behaviour of neuronal circuit dynamics, it is necessary to monitor brain activity in the awake, behaving animal. •  Licking to obtain water reward is an approach that is often used to measure an animal's decision during reward‐based behaviour tasks. •  In head‐fixed mice, licking produces stereotyped brain motion that interferes with two‐photon calcium imaging of neuronal activity. •  We describe a method to provide online optical correction of licking‐induced brain motion during two‐photon imaging using refocusing with an electrically tunable lens. •  Online correction of licking‐induced brain motion improves the measurement of neuronal activity during reward‐based behaviour. Abstract  Two‐photon calcium imaging in awake, head‐fixed animals enables the measurement of neuronal activity during behaviour. Often, licking for the retrieval of water reward is used as a measurable report of the animal's decision during reward‐driven behaviour. However, licking behaviour can induce severe motion artifacts that interfere with two‐photon imaging of cellular activity. Here, we describe a simple method for the online correction of licking‐induced focus shifts for two‐photon calcium imaging of neocortical neurons in the head‐fixed mouse. We found that licking causes a stereotyped drop of neocortical tissue, shifting neurons up to 20 μm out of focus. Based on the measurement of licking with a piezo film sensor, we developed a feedback model, which provides a corrective signal for fast optical focus adjustments with an electrically tunable lens. Using online correction with this feedback model, we demonstrate a reduction of licking‐related focus changes below 3 μm, minimizing motion artifact contamination of cellular calcium signals. Focus correction with a tunable lens is a simple and effective method to improve the ability to monitor neuronal activity during reward‐based behaviour.