1314, the Bishop allowed from Utrecht to build a wooden, Saint Pancras consecrated chapel on the 'Hoogeland'. This chapel was soon replaced by a simple stone church, which was soon too small again due to the strong growth of Leiden. In 1336 the church was elevated to the status of a collegiate church . In 1377, work began on building a new large church. The priest's choir was completed in 1391 and the ambulatory in 1415. With the construction of the Holy Cross Chapel in 1436, an approach to the south transept was built. Between 1432 and 1456 the aisles were enlarged. Due to the lack of funds in the chapter of the pen, the work came to a standstill at times. The transept was completed in its current dimensions around 1500 .
In 1470 the Pope released the chapter from the diocesan power of the Bishop of Utrecht . This measure is to be seen in connection with plans to elevate Leiden to the bishopric and the Pankratiusstift to the cathedral chapter. However, the increase in Reformation influences in Leiden marked the end of these plans. In 1535 the construction of the church was stopped, and in 1559 a new bishopric was established in Haarlem . In 1566 the Pankratius Church - and especially its splendid furnishings - were badly damaged in the iconoclasm . In 1572 the church passed into Protestant hands.
Until the middle of the 19th century, the church deteriorated increasingly. It was thoroughly renovated between 1840 and 1903. On this occasion, some of the 15./16. The construction phases that were no longer carried out in the 19th century were completed, so the church was now given stone vaults. Another renovation took place from 1952 to 1972. Today the church is used by the Protestant Church and the ecumenical student community as a place of worship and also serves as a venue for congresses, concerts and other events.
Organs
Historical organ
The current organ was built in 1637 by the organ builder Van Hagerbeer, reusing pipe material from the previous instrument from 1565. The instrument has 24 stops on two manuals and pedal (tuning: Werckmeister II).
An organ is currently being built in the church, which was built by the organ builders Willis & Harrison for St Mark's Church in Birkenhead (Great Britain). The instrument is arranged in the late romantic style. It has been restored and some typical registers have been added. The instrument is initially set up with 37 registers on three manual works and a pedal. In a further step, the instrument is to be supplemented by a fourth manual (solo work with a total of 13 stops); In addition, the pedal is to be expanded by 7 registers (registers without numbering are the planned registers in the future.)