Heritage Baptist College and Heritage Theological Seminary came into existence in March 1993. Negotiations between Central Baptist Seminary, Toronto, and London Baptist Bible College and London Baptist Seminary, London, which began in September 1992, concluded with amalgamation. In March 1993, the new Board met for the first time and adopted the name Heritage Baptist College and Heritage Theological Seminary. Classes at the new school began in September 1993 on the main campus in London and at the extension centres in Toronto and Bracebridge.

The roots of Heritage are deeply embedded in the history of the two former schools. Central Baptist Seminary and Bible College began in 1949 in Forward Baptist Church, Toronto, under the direction of President Jack Scott and Dean W. Gordon Brown. Until the mid-1980's, Central provided both undergraduate and graduate theological education from several Toronto locations. More recently, the school existed solely as a seminary and was relocated to Gormley, Ontario. Central served primarily the Fellowship Baptist movement in Canada and graduated 873 alumni who are serving in a great variety of ministry settings throughout the world.

London Baptist Seminary began in 1976 in Central Baptist Church, London, under the direction of President Gerry Benn and Dean of Students Marvin Brubacher. From its inception until the merger, the school provided undergraduate and graduate theological education. In 1981, the name was changed to London Baptist Bible College and London Baptist Seminary to reflect the two levels of education, and the school moved to its 30 Grand Avenue location. The Bible College and Seminary served a variety of baptistic church groups and graduated 583 alumni into many professional and lay ministries.

 On April 28, 1995, Heritage took possession of 7.1 acres at the corner of highways #401 and #24 in Cambridge. Renovations to the Academic Building were completed, residence buildings were under construction, and classes had commenced by the grand opening of the new campus on October 13, 1995. Ground was broken for the Heritage Community Centre on August 8, 1997. Most of the second floor was ready for use by the dedication service on September 26, 1998. The building was completed by the grand opening on October 28, 2000. On November 15, 2000, the purchase of 4.9 acres adjacent to the property was finalized. This will allow for future expansion of the facilities. 

 In the spring of 2001, the Heritage Board added the business name of Heritage College & Seminary for marketing purposes.

Heritage currently has over 2,200 graduates scattered around the world. This number includes alumni of Heritage College & Seminary, Central Baptist Seminary, London Baptist Bible College and London Baptist Seminary.

On May 9, 2003, Heritage celebrated its 10th anniversary with a dinner for over 300 guests. In his address, President Brubacher said, "We have only just begun. Can you imagine what God could do in the next 10 years? Just think of the graduates serving all over the world; the churches that are going to start; the tribes and people groups around the world that are going to be reached. We have so many more dreams for Heritage."