Trinity College Kirk was a royal collegiate church in Edinburgh, Scotland. The kirk and its adjacent almshouse, Trinity Hospital, were founded in 1460 by Mary of Guelders in memory of her husband, King James II who had been killed at the siege of Roxburgh Castle that year. Queen Mary was interred in the church, until her coffin was moved to Holyrood Abbey in 1848.

The original church design was never completed. Only the apse, choir (with aisles) and transepts were completed.

The church was located in the valley between the Old Town and Calton Hill, but was systematically dismantled in 1848 due to the construction of Waverley Station on its site. Although its stones were numbered in anticipation of rebuilding and were stored in a yard on Calton Hill, by 1872, when a replacement church was built on the newly formed Jeffrey Street, only a third were left which were used to construct a version of the choir and apse which was the hall of the new church.

The church was built of local sandstone from a quarry which was discovered only 500m to the west at the site of the Scott Monument on Princes Street. It was created in the cosmopolitan Scottish late Gothic style. As was the taste of the time, water was discharged from the roof via gargoyles. Unusually it is said the church had several monkeys within its decorations.

Trinity College comprised Trinity College Church, Trinity Hospital, and the Manses of the Prebendaries. The foundation of the college was for a provost, eight prebendaries and two clerks each being assigned particular benefices and land for their support. Income was derived from several sources in Scotland, either by the endowment of Mary of Guelders (from her own allotted incomes), or added later. Incomes were received from Uthrogal, a leper colony at Monimail in Fife, and the parish church of Easter Wemyss in Fife. In 1502 a Dean and Sub-Dean were appointed, their stipends paid from the parish of Dunnottar in Kincardineshire. In 1529 incomes were added from the parishes of Soutra, Fala, Lampetlaw, Kirkurd, Ormiston and Gogar.

The church and hospital of Soutra Aisle dedicated to the Holy Trinity, was held as a prebend of the chancellor of St Andrews. In 1459/60 the chancellorship was vacant allowing the dowager queen to supplicate Pope Pius II for the annexation of Soutra to her Trinity College foundation – the sanctioning bull was published on 23 October 1460. Queen Mary of Guelders (widow of James II) issued a Royal charter on 25 March 1462 detailing the constitution for Trinity College in which the provost was to hold Soutra church as a prebend but had to maintain three bedesmen in the Soutra hospital. John Halkerston was made Master of Works.

In August 1463 Pope Pius II declared by Papal bull that religious visitors to the church during the feast of the Holy Trinity on 10 July and the following eight days, over the next five years, would be granted a plenary indulgence, if they contributed to the fund for completion of the building according to their financial ability. The money was to be put in a locked box with two keys kept by the Provost and the Papal Collector for Scotland. A third of the receipts were to be given to the Catholic church for its general work.

The church was famed for its triptych altarpiece by Hugo van der Goes completed in 1479, now displayed in the National Gallery of Scotland. The four surviving panels depict James III, King of Scots, flanked by St. Andrew and his son, the future James IV, and his wife, Margaret of Denmark. The donor, the first Provost of the Trinity foundation, Edward Bonkil, and his coat of arms also feature.