This book constitutes the proceedings of the 46th International Conference on Application and Theory of Petri Nets and Concurrency, PETRI NETS 2025, held in Paris, France, during June 22-27, 2025. The 21 full papers and 1 short paper included in this book were carefully reviewed and selected from 48 submissions. They deal with topics such as composition and synthesis; workflow nets; process mining; model checking; communication & concurrency; timed and stochastic Petri nets; etc. The proceedings also include one invited talk in full paper length.