When learning goal-directed behaviours, new associations are made to achieve the desired motor output. The secondary motor cortex (M2), a frontal area of the rodent cortex, is a key region for transforming sensory information into a motor output. M2 has also been linked anticipation, impulse control, and short-term memory. Yet, our understanding of how M2 is involved in goal-directed behaviours remains lacking. Here, we used widefield, calcium imaging to measure cortical activity as mice learnt to discriminate two tactile stimuli. During learning of this goal-directed sensory-discrimination task, cortical activity patterns changed as the stimuli became behaviourally relevant. In particular, the medial secondary motor cortex (mM2), a subregion of M2, demonstrated large change in behavioural encoding throughout learning. To test the influence of whether these learning-induced changes in mM2 were driving learning of the task, we used an optimised channelrhodopsin expressed in interneurons (mDlx-oChIEF) to optogenetically supress mM2. Photo-inhibition of mM2 throughout learning resulted in faster rule acquisition, suggesting a direct involvement of mM2 in learning of goal-directed sensory-discrimination. Together, these findings provide greater understanding of cortical plasticity during learning, with mM2 playing an important role in influencing learning of goal-directed sensory discrimination.