Gold nanoparticle (AuNP)-assisted delivery of proteins/drugs to cells or in vivo systems has long been studied. However, their interaction with in vivo mimicking organoids is still largely unknown. Here, we conjugated brain-derived neurotropic factor (BDNF) to the AuNP surface and monitored how AuNP–BDNF interacts with cerebral organoids. Data suggest that AuNP–BDNF can successfully enter cerebral organoids and can be found up to 15.21 µm inside cerebral organoids. AuNP–BDNF does not induce significant cytotoxicity to cerebral organoids at concentrations up to 2 nM and increases the expression of 75 genes compared to control cerebral organoids. These data suggest the successful delivery of BDNF through AuNP–BDNF conjugation in cerebral organoids, and the conjugation can affect its differentiation.