Founded by Annie (Blois) Smith, the museum is housed in what was the old St. John Anglican Church building. The church was built in about 1861 on what is now Lake Thomas Drive, and was moved to its present site in 1893. The church was moved by horse and wagon in two sections to a more central location on what is now 2463 Rocky Lake Drive.
The museum moved into the church building when the church was sold in 1991 to what is now the Waverley Ratepayers Association. The new St. Thomas church in Fall River replaced the old church in Waverley when the congregation outgrew its facilities. St. Thomas church is now part of the Parish of Fall River.
Before moving into the church building in Waverley, the museum was situated in a house called the Smith House on the corner of Cobequid Road and Rocky Lake Drive. The house was later expropriated by the government and removed to make a safer highway intersection, leaving the museum with no place to go. At their annual meeting, the Waverley Ratepayers Association voted that the church be bought with the intention to have a facility for the museum.
Soon after the village bought the church building, the Waverley Heritage Society started work. The church’s sanctuary was converted into a museum, using the pews and kneelers for tables, shelves, and display cases. The work crew was soon ready to move the Smith house contents to their new home and the Waverley Heritage Museum was born!