Metal-based engineered nanomaterials (ENMs) have potential to revolutionize diagnosis, drug delivery and manufactured products, leading to greater human ENM exposure. It is crucial to understand ENM pharmacokinetics and their association with biological barriers such as the blood-brain barrier (BBB). Physicochemical parameters such as size and surface modification of ENMs play an important role in ENM fate, including their brain association. Multifunctional ENMs showed advantages across the highly regulated BBB. There are limited reports on ENM distribution among the blood in the brain vasculature, the BBB, and brain parenchyma. In this study, ceria ENM was used to study the effect of size on its pharmacokinetics. Four sizes of ceria ENMs were studied. Five nm ceria showed a longer half-life in the blood and higher brain association compared with other sizes and 15 and 30 nm ceria had a higher blood cell association than 5 or 55 nm ceria. Because of the long circulation and high brain association of 5 nm ceria compared with other sizes, its distribution between the BBB and brain parenchyma was studied. The in situ brain perfusion technique showed 5 nm ceria (99%) on the luminal surface of the BBB rather than the brain parenchyma. For biomedical applications in the central nervous system (CNS), it is vital to develop stable and biocompatible ENMs and enhance their uptake by taking advantage of their unique properties. Cross-linked nanoassemblies entrapping iron oxide nanoparticles (CNA-IONPs) showed controlled particle size in biological conditions and less toxicity in comparison to Citrate-IONPs. CNA-IONPs considerably enhanced MRI T2 relaxivities and generated heat at mild hyperthermic temperatures (40 ~ 42°C) in the presence of alternating magnetic field (AMF). Numerous researchers showed mild whole body hyperthermia can increase BBB permeability for potential brain therapeutic application. Compared to conventional hyperthermia, AMF-induced hyperthermia increased BBB permeability with a shorter duration of hyperthermia and lower temperature, providing the potential to enhance IONP flux across the BBB with reduced toxicity. Overall, ENMs with optimized physicochemical properties can enhance their flux across the BBB into the brain with desirable pharmacokinetics, which provide great potential for diagnosis and therapy in the CNS.