The church was built in the Baroque style between 1613 and 1615 on the site of an older Gothic style church, erected in the early 15th century by the Augustinian Order. In 1598, the old church was acquired by the Jesuits and thus became the first Jesuit church in the Slovene Lands and one of the first in Inner Austria. The interior was designed by the Italian architect Francesco Robba and the Slovene painer Luka Mislej. After the Ljubljana earthquake of 1895, the church was renovated by the Linz-based architect Raimund Jeblinger, while the interiors were remodelled by Janez Šubic. Nevertheless, much of the original Baroque style has remained intact.
On the side of the church, there is a column, erected in 1682 to commemorate the Habsburg victory against the Ottoman Turks in the battle of Saint Gotthard. The column, dedicated to the Virgin Mary, was designed by the Salzburg-based artist Wolf Weisskirchner.
In the late 1920s, the square in front of the church was renovated by the famous Slovene architect Jože Plečnik and in the early 1950s again by the architect Boris Kobe. Opposite to St. Jacob's Church, there is the Gruber Palace which houses the Slovenian National Archives.