From a faithful few, St. Andrews Free Church has become a thriving student church.

St. Peter's Free Church, Dundee, planted St. Andrews Free Church in September 2001. The need was seen through several St. Andrews students travelling the thirteen miles to Dundee for the strong biblical teaching in St. Peter's Free Church. For two years, from 2001, the group met at 4pm every Sunday in Martyrs' Church of Scotland. The numbers began to grow steadily, but in the long summer months were often sustained by just a few PhD students and their families.

In September 2003, Alasdair I. MacLeod was appointed minister of the congregation. The Church then moved to two Sunday services, (11am and 6pm), meeting in a Divinity lecture room in the morning, and Martyrs' Church of Scotland in the evening. The lecture room provided a temporary building, but the location was not ideal. In the January of the following year (2004), the congregation moved to meeting in a Boys' Brigade Hall in the morning. This building provided a better environment for Sunday morning services.

The Church saw rapid growth in the number of students attending following the appointment of Alasdair. A fulltime Pastoral Assistant, Matt Ford, was also appointed in August 2005, serving for three years and starting the ID Youth Group.

With growing numbers, from November 2009 the Church has moved its morning service to larger premises: the Baptist Church building on South Street.