The canons that belonged to the collegiate chapter of Saint Pancras were predominantly derived from ancient families and mostly of nobility.

On the advocacy of Charles the Bold, Pope Paul II granted the chapter of Saint Pancras' exemption on February 24, 1470.

Construction of the new church in the Gothic style began around 1470 and dendrological evidence indicates that the roof of the ambulatory was completed shortly after 1472, with that of the transepts and the choir by the end of the 15th century.

However, at the episcopal reorganization of 1559, the intended bishop's seat eventually fell to the Grote or Sint-Bavokerk in Haarlem.

The St Pancras became known as the Hooglandse Kerk and saw its first Protestant service in July 1574 in a much-changed interior: White-washed walls, plain transparent glass, seats for the congregation and no statuary or altars.

The original three parishes of the Pieterkerk, the St Pancras church, and the Vrouwenkerk were subsumed in the Dutch Reformed Congregation of Leiden and used as needed, which included grain storage during Leiden's siege in 1574 and quartering of troops in 1618 at the height of the dispute between followers of Armenius and Gomaris.

in 1665, the Hooglandse Kerk received a new west portal, executed in a mix of classical and gothic elements.

Seventeenth-century representations of the church indicate that its exterior is by-and-large the same as it is in the early 21st century: A tall gothic choir and transept, a much lower nave, and a relatively short bell tower, the top part of which is clad with wood.

By the early part of the 19th century, the church is almost completely ringed by these small houses, some of which have been subsequently demolished and others renovated.

The Hooglandse Kerk continues to hold church services; the Ecumenical Leiden Students Ekklesia worship there every Sunday.