Republished four times and widely distributed, her doctoral thesis on relations between the State and private teaching establishments linked by contract to the public sector has become the standard reference work in that area.

She was closely involved in discussions concerning and often the driving force behind the legislative and statutory changes which, over a period of two decades, shaped the legal framework which provides for balanced relations between the State and the private establishments linked by contract to the public education service.

During her first term of office, her work focused on an area whose importance for the future is still underestimated, given the predominance of economic issues: a citizens' Europe.

In August 1997 Fontaine published a guide to community aid schemes, entitled L'Europe de vos initiatives, and then in October 1998 a layman's guide to the Amsterdam Treaty entitled Le traité d'Amsterdam, à l'attention de ceux qui aimeraient s'intéresser à l'Europe si elle était moins obscure (the Amsterdam Treaty for those who would like to take an interest in Europe but find it difficult to understand).

Standing against Mário Soares for the post of President of the European Parliament, she was elected by a majority of the votes cast in the first round on 20 July 1999.

A profile by The Economist from that time described her as "a consensus-seeker, coalition-builder, conciliator ... nowhere more at home than in the Byzantine corridors of Europe, canvassing cross-party support, flashing her smile, teasing out compromise".

In 2007, Fontaine led an unsuccessful campaign to press for French to be designated the European Union's benchmark legal language.