This book constitutes the proceedings from the 31st IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems, AUTOMATA 2025, held in Lille, France, during June 30–July 2, 2025. The 11 full papers and 4 invited papers presented in this proceedings were carefully reviewed and selected from 19 submissions. The AUTOMATA series is the official annual event of IFIP WG 1.5, the Working Group 5 (on Cellular Automata and Discrete Complex Systems), of the Technical Committee 1 (on Foundations of Computer Science), of the International Federation for Information Processing (IFIP). AUTOMATA is an annual, international, multidisciplinary conference for experts in cellular automata and complex dynamic systems.