This book constitutes the refereed proceedings of the 12th International Conference on Brain Informatics, BI 2019, held in Haikou, China, in December 2019.The 26 revised full papers were carefully reviewed and selected from 36 submissions. The papers are organized in the following topical sections: cognitive and computational foundations of brain science; human information processing systems; brain big data analysis, curation and management; informatics paradigms for brain and mental health research; and brain-machine intelligence and brain-inspired computing. Also included is a special session on computational social analysis for mental health.