Intracortical microstimulation (ICMS) has demonstrated the potential to restore vision and hearing by stimulating relevant cortical regions in both animals and humans, offering significant clinical promise for sensory restoration. While the neuronal response to ICMS has been extensively studied at the cellular level through electrophysiology and two-photon (2P) imaging, the response of non-neuronal cells, particularly microglia, as well as the effects of ICMS on blood-brain barrier (BBB) integrity remain poorly understood. In this study, we applied ICMS under 2P imaging in dual-reporter mice, with green fluorescent protein labeling microglia and a red fluorescent Ca2+ indicator labeling neurons. We also monitored vascular dye leakage to assess BBB integrity throughout the experiment. Using clinically relevant waveform parameters, we tested a range of current amplitudes. Surprisingly, we found that microglia responded rapidly, within 15 minutes of stimulation, by converging their processes (MPC) on areas of high neural activity. The prevalence of MPC increased with higher current amplitudes, but intriguingly, it did not correlate with the strength of the local electric field. Additionally, vascular dye penetration into brain tissue was higher in stimulated animals than in controls and increased with current amplitude. This study reveals a rapid microglia and BBB response to ICMS that has not been reported previously, underscoring the need for further research to fully characterize the biological response to ICMS and establish improved safety standards.