This book constitutes the refereed proceedings of the International Workshop on Intelligent Agents in Science and Engineering (IASE 2025), held in conjunction with the 28th European Conference on Artificial Intelligence (ECAI 2025), in Bologna, Italy, in October 2025.The 6 full papers presented in this book were carefully selected and reviewed from 8 submissions. These papers have been organized in the following topical sections: Part I: Theoretical Foundations and AlgorithmsPart II: Agent-Based Modeling and Framework AnalysisPart III: Intelligent Agents in Biomedical ApplicationsPart IV: Intelligent Agents in Engineering Systems