The research arm of UP Baguio is the Cordillera Studies Center (CSC), internationally known for its excellent record in ethnic and interdisciplanary research programs. Faculty workgroups now undertake research on the following themes: local literature, natural products and biodiversity, environmental management, urban studies, local governance and developments, and ethnic studies.

UP Baguio supports extensive regional, national and international linkages for collaborative research and publication projects as well as scholarly exchange through the initiatives of CSC and the colleges. Its social science research program aims at comprehensive and in-depth understanding of regional communities, and provides input to policy and planning in areas such as local autonomy and natural resource managements. Its contributions to basic research in the natural sciences explore new theoretical directions and practical applications, highlight innovative technologies, and build on indigenous mathematical as well as biological knowledge systems. In the field of humanities, a research program is ongoing for the retrieval, annotation and translation of extant Cordillera and Northern Philippine Literatures. Researches in the management sciences have focused on autonomy, entrepreneurship, women and health among others. Researches in physical education include studies on physical education principles and actual practices of players, coaches and students especially in the highlands.