St John's has it's origins in a mission school which was founded in Stonefold village along with others at Grane and Musbury in 1836 by the Rev. William Gray, vicar of Haslingden. Being built near Black Lane Head it could provide for the villagers of Stonefold, Rising Bridge, Black Lane and Sherfin. By the 1870's the mission school building was suffering from damp and was to small for the 120 pupils who attended. To replace it the iron church and school was built on land across the road from the present church. Built at a cost of £600 the church could accommodate 230 people and the school 200 scholars.

In early 1884 Miss Martha Turner of Carter Place gave £3,000 to Canon Champneys, vicar of Haslingden to build a permanent church. The site of the new church was beside the highway from Haslingden to Accrington to the south of Rising Bridge on land which was given by Mr. H. W. Worsley-Taylor of Moreton Hall. The foundation stone was laid on 13th September 1884 by Mr. W. Turner of Westlands, Manchester, a nephew of Miss. Turner.

The iron church held it's last service on 16 May 1886 but the school was in use for a further eight years. The new church, which had seating for 342, was along with the burial ground consecrated on the 21st May 1886 by Bishop Moorhouse, Bishop of Manchester.

From 1886 to 1889 the church was served by the vicars and curates of St. James, Haslingden, until on the 18th October 1889, when a new parish was formed out of that of St James the Great, Haslingden with Rev. Richard Parker a curate of St. James being appointed first vicar.

The old school was replaced by a new building which was built on land given by Mr. H. W. Worsley-Taylor and was on Rising Bridge Road at the rear of the new church. The foundation stone was laid was on 1st July 1893 and the school opened in May 1894, the cost being approximately £2.500.

In 1982 the Rev. Thomas Bill became the joint vicar of St John's and St Peter's, Accrington. When Rev. Bill left the parish in 1989 it became a Joint Benefice under Rev. Roger Smith. the vicar of St James the Great, Haslingden.

The church held it's last service at the Harvest Festival on 30th September 2001 after insurance companies refused cover because of serious structural problems. Faced with a repair bill for £40,000 to rectify serious problems with a crumbling roof and the electrical system it was decided in 2003 to sell the Grade 2 listed building and it as now been restored as a private property.

Church registers date from 1886 with the first burial taking place in July that year. The first baptism was in 1889 and the first marriage in 1890. The registers are now on deposit at Lancashire Record Office.