Phayao University was established based on a Cabinet resolution on June 20, 1995, which approved the "Project for Expanding Educational Opportunities to Regional Areas (Phayao Province) of Naresuan University." On October 8, 1996, the Cabinet decided to rename it Phayao University. The current teaching facilities are located in Mae Ka Subdistrict, Mueang District, Phayao Province. Phayao University received approval from the Ministry of the Interior and Phayao Province to use the land for the university’s campus. The university first admitted students into the fields related to science and technology in the academic year 2000, offering three programs: Plant Science, Fisheries, and Agricultural Industry. The curriculum was administered by the Academic Office of Naresuan University, Phayao Campus.
On June 22, 2001, the Academic Office of Naresuan University, Phayao Campus, reorganized its administration into three academic groups: Information Technology, Arts, and Science and Technology. The Science and Technology Group was responsible for managing the three programs: Plant Science, Fisheries, and Agricultural Industry. Students in Agricultural Industry were required to transfer to Naresuan University in Phitsanulok for their third and fourth years. Starting from the 2005 academic year, the university planned to admit students into Chemistry and Biology programs, expanding the Science and Technology Group to five programs.
On June 28, 2004, the university restructured its administration into several academic units, including the Faculty of Agriculture, Natural Resources and Environment, the Faculty of Information Technology and Communication, the Faculty of Management Science and Information Science, the Faculty of Health Sciences, the Faculty of Science and Technology, and the Faculty of Engineering. According to the resolution of the Naresuan University Council at its 114th meeting (4/2547) on August 24, 2004, the Faculty of Agriculture, Natural Resources and Environment was upgraded to the Faculty of Agriculture and Natural Resources with Dr. Santhiwat Pitakphon as the first head of the faculty, making it equivalent to a department.
In the 2009 academic year, the Faculty of Agriculture and Natural Resources introduced two more programs: a Bachelor of Science in Agriculture (Animal Science) and a Bachelor of Science in Industrial Crop Production. Since the 2010 academic year, the faculty began offering all four years of the Agricultural Industry program at Phayao University.
On July 17, 2010, Phayao University was upgraded to an autonomous public university, no longer part of the government sector, and was renamed "Phayao University." As a result, the Faculty of Agriculture and Natural Resources became a faculty equivalent to a college, and the faculty was renamed the Faculty of Agriculture and Natural Resources. The current dean is Associate Professor Rattana Attapanyo.
The Faculty of Agriculture and Natural Resources at Phayao University is focused on improving the quality of life for the population, particularly by integrating knowledge and innovations in agricultural science and technology, animal science, fisheries, agricultural industries, biotechnology, industrial crop production, and natural resource management with local agricultural wisdom. The goal is to adapt to the geographic, economic, and social conditions of the upper northern region. This not only contributes to the economic development of the upper northern region but also helps reduce the costs for students who graduate from the region and wish to study agricultural and natural resource sciences without having to move to universities in central or other regions.