Microfluidic BBB‐on‐a‐chip models (μBBB) aim to recapitulate the organotypic features of the human BBB with great potential to model CNS diseases and advance CNS therapeutics. Nevertheless, their predictive capacity for drug uptake into the brain remains uncertain due to limited evaluation with only a small number of model drugs. Here, the in vivo brain uptake of a panel of nine radiolabeled compounds is evaluated in Swiss‐outbred mice following a single intravenously administered dose and compared against results from the microfluidic μBBB platform and the conventional Transwell BBB model. Radioisotopic measurements are employed to calculate brain‐to‐plasma concentration ratios (B/P) of the compounds both in vivo and in vitro. The in vitro‐in vivo correlation plots of the B/P ratios revealed a strong positive correlation (r = 0.8081, R2 = 0.6530) for the μBBB, suggesting a high degree of predictive ability for drug permeability into the brain. In contrast, the Transwell assay showed a weaker in vitro‐in vivo correlation (r = 0.6467, R2 = 0.4182). Finally, brain uptake of radiolabeled, brain‐targeted, angiopep2‐conjugated nanoparticles (ANG2‐NP) is assessed in the μBBB and results mirrored the in vivo uptake, while the Transwell model failed to resolve the differences between the targeted and non‐targeted NPs.