Fottrell was born on 6 February 1849 and educated at Belvedere College and the Catholic University, where he was president of the Literary and Historical Society. After training as a solicitor at the King's Inn Law School from 1865, he joined his father's firm of George D. Fottrell & Sons at 46 Fleet Street, Dublin. In 1872, he married Mary Watson, with whom he had one son and five daughters. He quickly established himself within Dublin's emerging Catholic professional class at a time when its influence over Irish public affairs was growing. Recent study of the Catholic elite of this period has demonstrated the importance of the university question to its ‘cultural and political awakening’. In educational matters, Fottrell was a secularist who wished to develop what he described as ‘a free and independent lay Catholic public opinion’. He was critical of reforms that tended to tighten the grip of ecclesiastical schools upon Catholic higher education and argued that sufficient funding for the Catholic University in Dublin was necessary to enable its graduates to compete on an equal footing with the predominately Protestant graduates of Dublin University. Alongside T.D. Sullivan and John Dillon, Fottrell took a leading role in the Catholic University's Bono Club, which aimed to create common ground between the ecclesiastical establishment and the educated laity, and Fottrell was assured by Cardinal Newman that
You will be doing the greatest possible benefit to the Catholic cause all over the world, if you succeed in making the University a middle station at which clergy and laity can meet, so as to learn to understand and to yield to each other.
In 1872, Fottrell tried to formulate reforms that might prove acceptable to both Protestant and Catholic opinion by proposing two universities for Ireland – the Queen's University and an amalgamation of Trinity College, Dublin and the Catholic University. He argued that Gladstone's University Education Bill, which proposed a single university for Ireland, would fatally damage the higher education of Catholics because it would denude the Catholic University of students. In 1879, he advised Gladstone to provide endowments for lay professorships in the Catholic University so as to enable Catholic students to escape the influence of ecclesiastical schools. Fottrell pursued his interest in Irish university education for many years, becoming an organizer of the Catholic Lay Committee of 1903 and publishing an influential tract on the subject two years later.