Thomas Pelham, the Chief Secretary for Ireland, introduced a bill for the foundation of a Catholic college, and this was enacted by parliament.

[5] The present college was created in the 1790s against the background of the upheaval during the French Revolution and the gradual removal of the penal laws.

A number of the early lecturers in Maynooth, were exiles from France (such as sometimes called the French founding fathers, Professors Francois Anglade, André Darré, Louis-Gilles Delahogue, and Pierre-Justin Delort), also among the first professors was a layman James Bernard Clinch recommended by Edmund Burke.

Butler had been a Roman Catholic, and Bishop of Cork, who had embraced Protestantism in order to marry and guarantee the succession to his hereditary title.

[9] The land was donated by William FitzGerald, 2nd Duke of Leinster, who had argued in favour of Catholic Emancipation in the Irish House of Lords.

The building work was paid for by the British Government; parliament continued to give it an annual grant until the Irish Church Act 1869.

Over the next 15 years, the site at Maynooth underwent rapid construction so as to cater for the influx of new students, and the buildings which now border St Joseph's Square (to the rear of Stoyte House) were completed by 1824.

Laurence F. Renehan (1797–1857), a noted antiquarian, church historian, and cleric, served as president of St Patrick's from 1845 until 1857.

[12][13] For example, the Anti-Maynooth Conference was hosted in London in May 1845 by Conservatives, evangelical Anglicans and the Protestant Association to campaign against the Maynooth Grant.

[16] He was supported by such Maynooth figures as the college president, Daniel Mannix, and the Professor of Theology, Walter McDonald (1854–1920).

In An Linn Bhuí, the Irish-language journal of Co Waterford, O'Hickey's home county, Mícheál Briody, lecturer at the Languages Centre, Helsinki University, Finland, says that O'Hickey was a prominent member of the Gaelic League and fiercely in favour of compulsory Irish for the new University of Ireland, whereas Mannix, then President of St Patrick's College, Maynooth, together with most of the Catholic bishops, was opposed.

Briody says that the senate of the new university, one year after O'Hickey's sacking, agreed to Irish being compulsory for matriculation and not long after that Mannix was posted as the Archbishop of Melbourne in Australia against his own will.

Mannix, however, later became a strong supporter of Irish republicanism and something of a thorn in the side of the authorities both ecclesiastical and civil, in Australia as well as Britain.

After his 10-year term ended in 2004, he was replaced by John Hughes as president of Maynooth University and a new line of heads for the college.

The Maynooth Union was founded in 1895 during the centenary and the constitution agreed in 1896, to "foster a spirit of mutual sympathy between the College and its past students and friends", it hosts an annual reunion.

One of the side effects of the act to disestablish the Church of Ireland, was that Maynooth's governance and funding changed, leaving only the Bishops on the board of trustees.

[32] When the annual grant received by the college was increased threefold in 1845, the president at the time, Laurence Renehan, started much needed renovations.

[32] Augustus Welby Pugin was brought in to design new buildings, which included a library with high gothic windows and an open timbered roof, completed in 1861.

The tall wooden stacks and long center tables hardly changed for over a century, and daylight was considered sufficient to work by until 1970, when electric lighting was finally introduced.

These included documents from other Irish colleges (Alcalá, Santiago, and Seville) and administrative records dating back to the end of the sixteenth century.

[37] Since October 2011 all academic awards from the Pontifical University of Maynooth have been aligned to the Irish National Framework of Qualifications by the NQAI.

[38] As part of the Erasmus university exchange programme, Saint Patrick's College, Maynooth has bilateral agreements with Faculties of Theology in Belgium, Czech Republic, Finland,[39] France, Germany, Malta, Portugal, Slovakia, Spain (Salamanca) and Switzerland (Freiburg).

[45] The Shekinah Certificate and Diploma Spirituality - Applied Youth Ministry and Facilitation, delivered online and blended learning, is accredited by Maynooth,[46] the programmes evolved out of the Salesian, Shekinah Youth Retreat Training Course which commenced in 2005, and these programmes before 2016 were run with and awarded by All Hallows College, Dublin.

[52] Since 2010 at the Kilkenny campus a Certificate in Christian Studies[53] for lay Anglicans, in association with the Church of Ireland Diocese of Cashel and Ossory has also been accredited.

[59] Maynooth validates the Diploma in Pastoral Theology run in association with the Roman Catholic Diocese of Derry,[60] and the Drumalis Retreat Centre, in Larne.

[64] It is supported by the Benefact Trust, and provides a number of free and paid courses online and via a mobile phone app.

[65] Aimed at both groups and individuals Aspal provides courses in Parish Administration, Ministers of the Word and Eucharist, and pathways to ministry.

The graduation ceremony for the conferral of Pontifical University degrees normally takes place on the first Saturday after the October Reading Week each year in the college chapel.