In 1831 the Nova Scotia Baptist Education Society founded Queen's College. Acadia began as an extension of Horton Academy (1828), which was founded in Horton, Nova Scotia, by Baptists from Nova Scotia and Queen's College (1838). The College was later named Acadia College. Acadia University, established at Wolfville, Nova Scotia in 1838 has a strong Baptist religious affiliation. It was designed to prepare men for the ministry and to supply education for lay members.

The two major Universities of the day in Nova Scotia were heavily controlled by Denominational structures. King's College (University of King's College) was an Anglican School and Dalhousie University, which was originally non-denominational, had placed itself under the control and direction of the Church of Scotland. It was the failure of Dalhousie to appoint a prominent Baptist pastor and scholar, Edmund Crawley, to the Chair of Classics, as had been expected, that really thrust into the forefront of Baptist thinking the need for a College established and run by the Baptists.

In 1838, the Nova Scotia Baptist Education Society founded Queen's College (named for Queen Victoria). The College began with 21 students in January 1839. The name "Queen's College" was denied to the Baptist school, so it was renamed "Acadia College" in 1841, in reference to the history of the area as an Acadian settlement. Acadia College awarded its first degrees in 1843 and became Acadia University in 1891, established by the Acadia University Act.

The Granville Street Baptist Church (now First Baptist Church (Halifax)) was an instrumental and determining factor in the founding of the University. It has played a supporting role throughout its history, and shares much of the credit for its survival and development. Many individuals who have made significant contributions to Acadia University, including the first president John Pryor, were members of the First Baptist Church Halifax congregation. Similarly, the adjacent Wolfville United Baptist Church plays a significant role in the life of the university.

This was unique at the time, and a direct result of Baptists being denied entry into other schools that required religious tests of their students and staff.

In 1851, the power of appointing governors was transferred from the Nova Scotia Baptist Education Society to the Baptist Convention of the Maritime Provinces.

Clara Belle Marshall, from Mount Hanley, Nova Scotia, became the first woman to graduate from Acadia University in 1879.

Acadia student-athlete Edwin Borden who graduated from Acadia in 1892, and again with a Master’s degree in 1896, after which he went on to earn his Doctorate. He was Acadia’s first graduate of African descent, and was also a member of Acadia’s varsity baseball team. Borden is presumed to be among the first athletes of African descent at any Canadian university.

In 1966, the Baptist denomination relinquished direct control over the University. The denomination maintains nine seats on the University's Board of Governors.

On 4 January 2008, Dr. Gail Dinter-Gottlieb decided to step down as President and Vice Chancellor of the University before her term expired. Her resignation was effective 29 February 2008. Ray Ivany began his position as President and Vice-Chancellor on 1 April 2009.

Acadia's sports teams are called the Axemen and Axewomen. They participate in the Atlantic University Sports conference of Canadian Interuniversity Sport.

School spirit abounds with men’s and women’s varsity teams that have delivered more conference and national championships than any other institution in Atlantic University Sport. Routinely, more than one-third of Acadia’s varsity athletes also achieve Academic All-Canadian designation through Canadian Interuniversity Sport by maintaining a minimum average of 80 per cent.

Expansion and modernization of Raymond Field was completed in the fall of 2007 and features the installation of an eight-lane all-weather running track and a move to the same premium artificial turf used by the New England Patriots of the National Football League for its main playing field. The Raymond Field modernization was a gift to the university by friends, alumni, and the province. War Memorial Gymnasium also saw the installation of a new playing floor to benefit its basketball and volleyball teams.

The Memorial Gymnasium honours students who had enlisted and died in the First World War, and in the Second World War. Two granite shafts, which are part of the War Memorial Gymnasium complex at Acadia University, are dedicated to the university's war dead.