Flather attended Fox Primary School in London from 1962 to 1963, Hurst Court School in Hastings from 1963 to 1968, and won a scholarship to attend Rugby School from 1968 to 1972.
From 1973 to 1976, he took his BA in Politics, Philosophy, and Economics at Balliol College, Oxford, graduating with a first-class Honours B.A. After working as a journalist and in politics for several years, Flather returned to Oxford and Balliol in 1985 for the completion his MA and DPhil (PhD) research degree on modern Indian politics. He received the Political Studies Association annual award for the best dissertation in any field of political studies for his doctoral thesis in 1991. His research interests focus on Indian democracy since 1947 and more recently on anti-corruption strategies.Paul Flather, "Education Matters." British social attitudes: The fifth report. (Aldershot: Gower Publishing,1988): 17-34.
- "Pulling through: conspiracies, counterplots and how the SSRC escaped the axe in 1982." in: M. Bulmer (ed.), Social Science Research and Government: Comparative Essays on Britain and the United States (Cambridge and New York: Cambridge University Press, 1987), 353-72.
- "Should Mother Teresa accept money from the Mafia?" in: Alan Montefiore and David Vines (eds.) Integrity in the Public and Private Domains (New York: Routledge, 1999), 190-204.
- (ed.), Recasting Indian Politics: Essays on a Working Democracy, (London: Palgrave, 2002).
From the mid-1970s and throughout the 1980s, Flather worked as a journalist, first as a freelancer and film, art and book reviewer and later for a number of established regional, national, and international newspapers and media houses. Inter alia, he worked as reporter, correspondent, and editor on media such as the Sheffield Morning Telegraph, Yorkshire TV, BBC Television News, The Times, The Sunday Times, and Times Higher Education, where he worked as feature writer and correspondent, including foreign coverage, specialising in research and social sciences. In 1989, he served as deputy-editor on the New Statesman & Society magazine, commissioning, planning, editing, and writing editorials.
Flather served as press fellow at Wolfson College, University of Cambridge in 1984.
From 1986 to 1990, he was an elected member (regional councillor) of the Inner London Education Authority, chairing the Further and Higher Education sub-committee, with an annual budget of some £340 million. During his time as councillor, Flather also held membership posts at the Association of Metropolitan Authorities and the London Boroughs Association. He was elected to many national education bodies and from 1989 to 1993, he was member of the National Institute of Adult Continuing Education, chairing its public affairs committee until 1991.
In the early 1990s, Flather worked for four years for the Open Society Foundation setting up a variety of international Soros programmes and was founding Secretary-General, member of the Senate, and CEO of the Central European University which was originally set up in Prague, Budapest and Warsaw after the 1989 revolutions. Flather was responsible for 80 staff members and an annual budget of £15 million, for negotiations with governments and the CEU's policy development and central administration.
He was then recruited as new Director of International and External Affairs at Oxford University, a post he for five years until 2000. The directorate includes the responsibility for all international links, overseas scholarships, media relations, alumni relations, relevant University publications, information and communication, events, and community links. In addition, he served as secretary to the University's International Committee, as treasurer of the Europaeum, as Oxford's University representative to COIMBRA Group. He was also an advisor to Oxford Today and editor of Gazette News.
In 2000, Flather was appointed as Secretary-General of the Europaeum, an association of leading European universities, including Oxford, Leiden, Paris 1 Pantheon Sorbonne, Charles University, Prague, Jagiellonian University, Krakow, the Graduate Institute of International and Development Studies, Complutense University of Madrid, the University of Helsinki, Universitat Pompeu Fabra, Barcelona, Ludwig-Maximilians-Universität München, and the Institute of Political Studies, Catholic University of Lisbon as associate member. In 2017, the Europaeum welcomed the University of St Andrews and the Central European University as its newest members. Flather presided over the growth of the Europaeum, from the original three members when he joined the association, to a total of 13 in 2017. In his time as Secretary-General, he coordinated collaborative academic research, study, and teaching programmes for and between member universities. He was also editor of Europaeum Review, director of many research programmes, coordinator for joint study and degree initiatives, and he ran several annual summer schools, spring schools, graduate workshops, policy-making seminars, and classic colloquia. Furthermore, Flather fund-raised for the Europaeum's visiting professorships and scholarships programmes.
At Oxford University, he was Tutor to MPhil students and an Associate Fellow of Queen Elizabeth House, from 1986 to 1987, Fellow of Corpus Christi College from 1994 to 2000. He is Fellow of Mansfield College since 2001.
Throughout the 1980s, Flather worked with dissident movements in Central Europe and race equality groups in the UK. In 1985, at that time serving as Trustee of the Jan Hus Educational Foundation, he was arrested and expelled for smuggling books and giving underground lectures in Czechoslovakia. Among many other, prominent intellectuals such as Jacques Derrida, Jürgen Habermas, Charles Taylor, Ernst Tugendhat, Thomas Nagel, and Ernest Gellner, Flather was working with the Foundation to support academic dissidents and promote links between academics in Britain and Czechoslovakia. In 1998, he was awarded a Commemorative Medal by Václav Havel, then President of the new Czech Republic.
Flather also chairs the Noon Educational Foundation supporting Pakistani scholars to study at top UK universities, is on the editorial board of RoundTable journal, serves as chair of the British Organisation of People of Indian Origin, and remains involved with charities, civic bodies and race bodies.