The Federal University of Agriculture, Abeokuta, Ogun State, or FUNAAB, (FUNAAB) was established on 1 January 1988 by the Federal Government when four universities of technology, earlier merged in 1984, were demerged. This led to the creation of the first two universities of agriculture in Abeokuta and Makurdi.

On the same date, Professor Nurudeen Olorun-Nimbe Adedipe was appointed the pioneer Vice-Chancellor of the university. Professor Adedipe officially assumed duty on 28 January 1988. For many years the date which Professor Adedipe assumed duty was wrongly adopted as the foundation day. Following a revisit to the instrument setting up the university, a council decision at its 53rd statutory meeting in June 2010 reverted the foundation date to 1 January 1988 as prescribed by the law which established the university.

Prior to the emergence of FUNAAB, the Federal Government had established Federal University of Technology, Abeokuta (FUTAB) in 1983. Then, in 1984, it was merged with the University of Lagos and had its name changed to the College of Science and Technology, Abeokuta (COSTAB), before the demerger of January, 1988.

The university started off from the old campus of Abeokuta Grammar School, Isale-Igbein near the city centre. It completed its movement to its permanent site along Alabata Road in 1997.

At the initial stage, five colleges were introduced in the university in October 1988 as follows:

College of Agricultural Management, Rural development and Communication Studies (COLAMRUCS), which name was later changed to COLAMRUD (College Of Agriculture Management and Rural Development)
College of Animal Science and Livestock Production (COLANIM)
College of Environmental Resources Management (COLERM)
College of Natural Sciences (COLNAS)
College of Natural Science was reformed and redrafted into 2 colleges which are College of Physical Sciences (COLPHYS) and College of Biological Science (COLBIOS)

College of Plant Science and Crop Production (COLPLANT)
Two additional Colleges, College of Engineering (COLENG) and College of Veterinary Medicine (COLVET) were introduced in March, 2002. During the 2008/2009 session, the College of Agricultural Management, Rural Development and Communication Studies was split into two, with two new colleges emerging as follows:

College of Food Science and Human Ecology (COLFHEC)
College of Agricultural Management and Rural Development (COLAMRUD)
The newest college is College of Management Sciences (COLMAS)

The university is one of the three universities of agriculture in Nigeria, the other being in Makurdi (Benue State) and Umudike (Abia State). The university started at its mini-campus in Isale-Igbein in the heart of Abeokuta, the capital of Ogun State. In December 1997 it moved to its permanent site on a 10,000-hectare campus which is located next to the Ogun-Oshun River Basin Development Authority on the Abeokuta-Ibadan road in the North Eastern end of the city, 15 km from Abeokuta City Centre