The fruits of Euodia rutaecarpa (Euodiae Fructus, EF), the widely used traditional Chinese medicine, have various central nervous system effects. Alkaloids following as evodiamine (EDM), rutaecarpine (RCP) and dehydroevodiamine (DEDM) are the major substances in EF. The MDCK-pHaMDR cell monolayer model was utilized as a blood-brain barrier (BBB) surrogate model to study their BBB permeability. The transport samples were analyzed by high performance liquid chromatography and the apparent permeability coefficients (Papp) were calculated. EDM and RCP showed high permeability through BBB by passive diffusion, while DEDM showed moderate permeability with efflux mechanism related to P-glycoprotein (P-gp). EDM and RCP could also reduce the efflux of DEDM probably by inhibiting P-gp. The neuroprotective effects of the three alkaloids were then studied on the PC12 cell line injured by 1-methyl-4-phenylpyridinium ion (MPP+) or hydrogen peroxide (H2O2). EDM could significantly reduce MPP+ or H2O2-induced cell injury dose-dependently. RCP could increase the cell viability in MPP+ treated group while DEDM showed a protective effect against H2O2 injury. This study predicted the permeability of EDM, RCP and DEDM through BBB and discovered the neuroprotective substance basis of EF as a potential encephalopathy drug.