This volume constitutes the proceedings of the 13th International Conference on Combinatorial Optimization and Applications, COCOA 2019, held in Xiamen, China, in December 2019. The 49 full papers presented in this volume were carefully reviewed and selected from 108 submissions. The papers cover the various topics, including cognitive radio networks, wireless sensor networks, cyber-physical systems, distributed and localized algorithm design and analysis, information and coding theory for wireless networks, localization, mobile cloud computing, topology control and coverage, security and privacy, underwater and underground networks, vehicular networks, information processing and data management, programmable service interfaces, energy-efficient algorithms, system and prool design, operating system and middleware support, and experimental test-beds, models and case studies.