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.