Zion Presbyterian Church in Charlottetown, Prince Edward Island, was created in 1870 by the amalgamation of the congregations of the Free Church and the Queen's Square Church.

At the first meeting of the Free Church Presbytery of PEI on 20 July 1854, a preaching station was organized in Charlottetown and was ministered to by various students and ministers. In 1855, West River was disjoined from Strathalbyn and united with Charlottetown to form the Free Church congregation of Charlottetown. Growth was rapid and in 1856 West River was disjoined and the Charlottetown Free Church inducted its first incumbent minister, Rev. George Sutherland and opened its church on the corner of Prince and Euston Streets. Various moves to amalgamate with the Queen's Square congregation or with the congregation of the Kirk of St. James did not prevail until 1870 when the congregation had dimished and was without a pastor.

Although there had been a Presbyterian preaching station in Charlottetown as early as 1849 organized by R.S. Patterson, it was not until 1856 that the Presbytery of Pictou and P.E.I. constituted the Queen's Square congregation. At that time the old Temperance Hall on the north-east corner of Prince and Grafton was rented for services conducted by various Presbyterian ministers. In 1860 a new church opened on Richmond Street and the congregation thenceforth enjoyed a regular supply of preaching. With the departure of Rev. Alexander Falconer in 1869, both this congregation and that of the Free Church were without a minister and the two congregations united to form one congregation to be known as Zion Presbyterian Church. There was also some movement to amalgamate with the congregation of the Church of St. James but this never came to fruition.

Services were held in the Queen's Square Church while the Free Church was rented to the Methodists until their new church was completed. The Free Church would be opened again for services between 1878 and 1882 when the congregation overflowed the Queen's Square Church but it was eventually sold in 1882 along with the manse. The Queen's Square Church was enlarged and remodelled in 1879 and again in 1885 to accommodate 1000 worshippers. In 1913, the congregation relocated to the site of their new brick church on the north-west corner of Prince and Grafton Streets which was dedicated on 13 May of that year. The Richmond Street church was loaned to St. Dunstan's Catholic Church until the Basilica was completed in 1919 at which time the Diocese purchased it and it become the Holy Name Hall. It was eventually torn down to give way to the Basilica Rec Centre.

In 1925, the Zion congregation turned down Union with the Methodists and the Congregationalists by a vote of 300 to 212. Although 17 of the 19 members of Session resigned causing some disarrangement, this was temporary and the Church continues to flourish.