Ischemic stroke exacts a heavy toll in death and disability worldwide. After ischemic stroke, the accumulation of pathobiomolecules in the brain extracellular space (ECS) will exacerbate neurological damage and cognitive impairment. Photobiomodulation (PBM) has been demonstrated to improve cognitive function in Alzheimer’s disease mouse models by accelerating molecular transportation in the brain ECS. This suggests that PBM may have a potential role in the accumulation of pathobiomolecules in the brain ECS following ischemic stroke. In this study, we developed a PBM therapy apparatus with custom parameters. By evaluating the treatment effect, we identified that 755 nm was the optimal light wavelength for ischemic stroke in rats with transient middle cerebral artery occlusion/reperfusion. Extracellular diffusion and interstitial fluid (ISF) drainage were measured using a tracer-based magnetic resonance imaging method. Our results showed that PBM accelerated molecular transportation in the brain ECS and ISF drainage, promoting the clearance of pro-inflammatory cytokines and reducing the deposition of pathological proteins. Consequently, the infarct volume decreased and neurological cognitive function was improved. Besides, the acceleration of ISF drainage was achieved by reducing expression and restoring polarization of aquaporin 4 (AQP4) in the peri-infarct area. In summary, we demonstrated that PBM could alleviate ischemia–reperfusion injury and prevent post-stroke cognitive impairment by accelerating molecular transportation in the brain ECS, paving a pathway for ischemic stroke treatment via the light–ECS interaction.