Ischemic stroke (IS) commonly results in long-term disability, largely due to alterations in neuronal networks. In repeatable rodent IS model under naturalistic conditions, the difficulty of capturing single-cell neuronal activities and how this solves a long-standing challenge is still remained. Here, we combined a photothrombotic stroke model with head-mounted miniaturized two-photon microscopy (mTPM) to achieve longitudinal, real-time imaging of GABAergic neurons in the contralesional primary motor cortex (M1) in freely moving mice. We observed pronounced reductions in calcium dynamics in GABAergic neurons. These calcium dynamics emerged as early as day 3 post-stroke and persisted through day 19, despite no detectable gross motor deficits. Our findings highlight subtle cortical dysfunction persists despite normal gross motor function, underscoring the need for finer behavioral tests. This approach offered a powerful tool to bridge the gap between cellular-level dysfunction and macroscopic behaviors after focal ischemic stroke.