The blood–brain barrier (BBB) is a highly selective semipermeable border that separates the circulating blood from the brain and extracellular fluid in the central nervous system (CNS). In its neuroprotective role, the blood–brain barrier functions to hinder the delivery of many potentially important diagnostic and therapeutic agents to the brain. Overcoming the difficulty of delivering therapeutic agents to specific regions of the brain presents a major challenge to treatment of most brain disorders. Choosing the compounds that could penetrate BBB into the compound library targeting CNS is critical for CNS drug discovery. Based on the scientific literature, TargetMol collects 509 out of 5000 compounds as CNS-Penetrant Compound Library, which can be used for CNS-Penetrant related research and drug screening for CNS diseases.