Founded in 1953 by the late Fr William F Masterson SJ, Xavier University College of Agriculture is the second oldest among the colleges of agriculture in Mindanao and is the only Catholic College of Agriculture in the country.  It is one of the founding members of the Agricultural Colleges Association of the Philippines (ACAP).

1950s

• Offered BS Agriculture program with major fields in Agronomy and Animal Husbandry (1953)
• Manresa Farm was acquired (1956)
• Extension service began through the volunteer extension program (1957), where student volunteers were the first extension agents

1960s

• Agricultural Economics was offered as a major under the BS Agriculture program (1964)
• South East Asia Rural Social Leadership Institute (SEARSOLIN) was established (1964)
• Xavier Science Foundation was established (1968)
• Rural Communication Center, considered as the outreach arm of Development communication, was set up (1966)
• Institute of Market Analysis was established (1968)

1970s

• COCOFED Scholarship Program started
• College became co-ed (1975)
• Agricultural Engineering was offered as one of major fields in the College (1976)
• Food Technology and Development Communication were offered as majors under the BS Agriculture Program (1978)
• MS Agricultural Economics was offered under the Graduate School (1970)

1980s

• Food Technology Center and Appropriate Technology Center were established (1983)
• XU - Affiliated Non-Conventional Energy Center, a project funded by the Department of Energy, started (1988)
• Mindanao Support and Communication Center for Agrarian Reform and Rural Development (MinCARRD) was established (1988)

1990S

• Sustainable Agriculture Center was set up (1991)
• Year of Service Program was launched (1991)
• PeriUrban Vegetable Project (PUVeP) was started (1997)
• BS Agribusiness program was offered (1997)
• BS Agriculture program was accredited Level I by the Philippine Accrediting Association for Schools, Colleges and Universities (PAASCU) (1997)

2000s

• BS Agriculture program was accredited Level II by PAASCU (2005)
• Xavier University was recognized by the Commission on Higher Education (CHED) as a Center of Development in Agriculture Education (2009)

2010s

• BS Agriculture program was accredited and reaccredited Level III by PAASCU (2010 and 2015, respectively)
• Recognized as a Provincial Institute of Agriculture by CHED under the National Agriculture and Fisheries Education System (NAFES) (2012)
• Offered two modules in the Master of Public Management – Rural Development program of the Development Academy of the Philippines, in collaboration with UP Diliman and Ateneo de Manila – School of Government
• Recognized by CHED as a Center of Excellence in Agriculture Education (2016)