Until 2018 he served as the Secretary-General of the Europaeum, an association of leading European universities, and is Fellow of Mansfield College, Oxford.

His family fled Lahore, where his great-great-grandfather had founded hospitals, schools, colleges, and charities at partition settling in Delhi.

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.

After graduating from Balliol College, Oxford, Flather worked variously for the BBC, Times Newspapers, the New Statesman among other journals, before being elected as a full-time politician, chairing London's Post-Schools education committee.

[3] 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.

Over the years, Flather has given lectures all over the world, chairing sessions and coordinating workshops, conferences and summer schools all over Europe, including high-level sessions for the British Council on how to battle corruption, published many articles, chapters, edited collections, reports and books, and advised the EU on how to take forward is relations with India in the lead to the 50th anniversary of its independence.

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.

[6][circular reference] Flather speaks of his experience during this time here, while discussing restoring scholarship and academic from in Czech and Slovak nations.

Flather also chairs the Noon Educational Foundation supporting Pakistani scholars to study at top UK universities,[7] 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.

Flather received an Honorary Silver Medal of Jan Masaryk at the Czech Republic Ambassador's residence in London in November 2019.