St Pauls Yarra Glen has had a long association with the parish of St Johns Healesville in the Diocese of Melbourne. The earliest building at Healesville was a little paling church built at Healesville in 1869 and opened 1 January 1870. Once clergy were established at Healesville some years later they also officiated at services in Yarra Glen, Steels Creek and Christmas Hills.

A meeting was held at Yarra Flats Hotel on Saturday 10 July 1886 to discuss the building of an Episcopalian Church at Yarra Flats.  John Sayle  (1820-1901) chaired the meeting and a committee was formed of local residents. A block of land at the corner of Armstrong Grove and the Old Healesville Road (Melba Highway) was donated by Mr. John S. Woolcott, a Melbourne solicitor. The plans were to build in brick with provision for extensions to meet later requirements.

Fundraising events were organized during the next few months and in November 1887 it was announced that the contract for building the church was let to Mr Robert Lowman and Mr Shaw at a cost of £188 18s 6d, not including seats, fittings, etc. The ambitious plans of 1886 were modified to suit the budget and, instead of brick, the church was constructed of timber with a very high gable roof. It was opened on Thursday 19 April 1888 by the Bishop of Melbourne, Right Rev. Dr Goe.

The first baptism was conducted a month after the opening on 27 May 1888 with James Thomas Smedley, the fifth child of John Francis & Ellen Smedley (nee Foster.)

Reverend Holloway was the first to officiate at Yarra Glen, succeeded by Mr C. K. Cole and then Mr Harvey in mid-1890.

In August 1897 the Lilydale Express reported that a novel sight took place in the village last week when the Church of England was bodily removed into the centre of the township. A splendid site had been procured, which was further improved by a three-roomed parsonage.  The church was enlarged with a chancel and vestry in 1901 and by 1922 the three-room parsonage had been renovated or replaced by a vicarage. The site was exposed to strong north winds and by 1938 the building had a distinct lean and the high gable was causing some concern. Standing stays were erected by a working party of  L. J. Adams, F. Sadlier and W. Lawrence. Further reinforcing was carried out in 1950 by Sadlier and Lawrence.

The Reverend Haslem was the only vicar who resided in Yarra Glen. He was followed by a number of relieving ministers. Between 1942 and 1948 Reverend S. Muxworthy came from Healesville by train once a week with a bicycle on which he endeavoured to visit as many of the parishioners as he could. The vicarage was rented out as a domestic residence. In 1982 it was renovated and divided into a flat for rental and meeting rooms for the use of the church people.

St Pauls contains a number of memorials and special gifts presented by members of the congregation. Martin Boyd, the well-known author, presented a brass cross for the altar. There is a set of beautiful stained glass windows commemorating the three McLeod brothers who died at war: Leslie and Alexander in World War 1, and Othel (known as Keith) in the Second War. The two elder boys attended Sunday School when their father was the resident police officer at Yarra Glen.  Ralph Keets (1908-1971) carved the oak stand for the baptismal font and the brass bowl surmounting it was presented by the Ladies Guild.

Sources:  Mollie E. Smith, The History of St Pauls Anglican Church Yarra Glen, 1988; YG&DHS Newsletter no.21, August 2006