The University of Waikato began in 1956 after Hamilton locals launched a petition for a university to serve the needs of the South Auckland region. The group was led by Douglas Seymour, a barrister, and subsequently Anthony “Rufus" Rogers, a Hamilton GP and brother to long-time Mayor of Hamilton, Denis Rogers. Their campaign coincided with a shortage of teachers in the 1950s that prompted the New Zealand government to consider plans for a teachers’ college in the region. In 1960, the newly established Hamilton Teachers’ College opened its doors, and combined with the fledgling university (then a branch of Auckland University), began a joint campus on farmland at Hillcrest, on the city's outskirts.

In 1964, the two institutions moved to their new home, and the following year the University of Waikato was officially opened by then Governor-General Sir Bernard Fergusson.

At this time the university comprised a School of Humanities and a School of Social Sciences. In 1969 a School of Science (now the Faculty of Science and Engineering) was established. This was followed by the creation of Waikato Management School in 1972, Computer Science and Computing Services (which ultimately became the Faculty of Computing and Mathematical Sciences) in 1973, and the establishment of the School, now Faculty, of Law in 1990.

From the beginning, it was envisaged that Māori studies should be a key feature of the new university, and the Centre for Māori Studies and Research was set up in the School of Social Sciences in 1972. A separate School of Māori and Pacific Development was formally established in 1996. In 1999, the original Schools of Humanities and Social Sciences were merged to form the School (later Faculty) of Arts and Social Sciences. In 2010, the tertiary partnership was widened to include Te Whare Wānanga o Awanuiārangi in the Eastern Bay of Plenty.

In 2014, the university became smoke-free, disallowing smoking on campus and in university-owned vehicles.