Nanoparticles hold great promise as drug carriers for the central nervous system (CNS), however, knowledge about their biodistribution within the CNS remains fragmentary. To overcome this, we used poly(lactic-co-glycolic acid) (PLGA), a biodegradable polymer approved for the use in humans, to prepare nanocarriers and loaded them with bulky fluorophores. Thereby, we increased single particle fluorescence by up to 55-fold as compared to quantum dots. As a consequence, 70 nm PLGA nanocarriers were visualized in vivo by 2-photon microscopy, demonstrating that coating with pluronic F-68 (PF-68) significantly increased circulation time of PLGA nanoparticles in blood and facilitated their uptake by cerebral endothelial cells in mice. Using a novel ex vivo imaging protocol we unambiguously distinguished nanoparticles’ fluorescence from tissue auto-fluorescence and demonstrate they were taken up into late endothelial lysosomes. In summary, by increasing the brightness of clinically approved PLGA nanocarriers to a level which allowed in vivo tracking, we were able to demonstrate that PF-68 shifts the uptake of individual particles from macrophages towards endothelial cells. Our novel technological approach significantly improves the ability to evaluate tissue targeting of nanoscale drug-delivery systems in living organisms, thereby remarkably reducing the gap between their development and clinical translation.