Photon scattering has traditionally limited the ability of near-infrared spectroscopy (NIRS) to extract accurate, layer-specific information from the brain. This limitation restricts its clinical utility for precise neurological monitoring. To address this, we introduce an AI-driven, high-density NIRS system optimized to provide real-time, layer-specific oxygenation data from the brain cortex, specifically targeting acute neuro-emergencies. Our system integrates high-density NIRS reflectance data with a neural network trained on MRI-based synthetic datasets. This approach achieves robust cortical oxygenation accuracy across diverse anatomical variations. In simulations, our AI-assisted NIRS demonstrated a strong correlation (R2=0.913) with actual cortical oxygenation, markedly outperforming conventional methods (R2=0.469). Furthermore, biomimetic phantom experiments confirmed its superior anatomical reliability (R2=0.986) compared to standard commercial devices (R2=0.823). In clinical validation with healthy subjects and ischemic stroke patients, the system distinguished between the two groups with an AUC of 0.943. This highlights its potential as an accessible, high-accuracy diagnostic tool for emergency and point-of-care settings. These results underscore the system's capability to advance neuro-monitoring precision through AI, enabling timely, data-driven decisions in critical care environments.