Lipid nanoparticles (LNPs) have delivered RNA to hepatocytes in patients after intravenous administration. These clinical data support efforts to design LNPs that transfect cells in the central nervous system (CNS). However, delivery to the CNS has been difficult, in large part because quantifying on-target delivery alongside common off-target cell types in adult mice remains challenging. Here we report methods to isolate different cell types from the CNS, and subsequently present mRNA delivery readouts using a liver-detargeted LNP. These data suggest that LNPs without targeting ligands can transfect cerebral endothelial cells in mice after intravenous administration. Given the difficulty of crossing the blood–brain barrier, they also underscore the value of quantifying delivery in the CNS with cell-type resolution instead of whole-tissue resolution.