The first Anglican church (then called Church of England) in Lakefield was Christ Church, a lovely small stone church which was opened on Christmas Day in 1854. It wasn't long before the congregation outgrew Christ Church. In 1864, the decision was made to build a new church building rather than enlarge Christ Church.

The new church, which was named St. John the Baptist, was opened in 1866. The Rev. Vincent Clementi, who had arrived in Lakefield in 1863 and oversaw the building of the new church, served as St. John's first priest.

Until the early 1950s, Christ Church was used by St. John's as a location for Sunday School classes. Today, Christ Church is officially designated as a "Chapel of Ease" under the sponsorship of St. John's. It is used primarily as a community museum to honour the pioneers that established Lakefield as a thriving community on the Otonabee River. As well, occasional worship services are held at Christ Church during the warmer months.

Over the years, St. John's has experienced some important structural additions. The two-story brick rectory beside the church was completed in 1875. The Bell Tower and entrance-way were added to St. John's in 1884. It wasn't until 1953 that the parish hall was added; up to that time, Christ Church was used for St. John's Sunday school classes. The parish hall was enlarged and renovated in 1989, providing a much larger kitchen in addition to office space, a choir room, and other rooms. In 2012, an elevator was added to provide access to the two levels of the parish hall.

In 2010, the structure housing the church bell was struck by lightning. This caused a number of stones from the structure to fall and crash through the roof of the Queen street entrance-way. Restoration was completed within a few months.