The International Workshop on Petri Nets and Software Engineering (PNSE'2025) took place at June 23, 2025. The workshop is co-located with 46th International Conference on Application and Theory of Petri Nets and Concurrency (PETRI NETS 2025) in Paris, France. The workshop started in 1997 in Hamburg and emphasizes on the impact of software engineering in general and its development based on Petri nets. Therefore we have especially invited contributions that work on subjects that could be relevant for Petri nets, their application, supporting tools, etc. Results on other formalisms or semi-formal techniques are highly welcome. More information about the workshop can be found at: http://www.pnse.de/ This year we received 16 contributions for these proceedings. Each paper was reviewed by at least three referees. During the reviewing process the program comittee selected 8 contributions for publication. The workshop was organised in sessions with long and short presentations. The proceedings also contain the extended abstracts for the accepted poster contributions. We are glad that Yann Thierry-Mieg accepted our invitation to give a talk about Practical Lessons from Applying Large Language Models in Teaching, Development, and Research, where he explored practical applications including creating teaching materials, research ideas, writing code, and crafting formal documents. The international program committee of PNSE'25 was supported by the valued work of Enzo Erlich, Dominik Janssen, Marcin Piatkowski, and Marc Schmidt as additional reviewers. Their valuable work is highly appreciated. Furthermore, we would like to thank our colleagues in the PC and the local organization team in Paris for their support.