During his career as civil servant, Pieter Jan Kuijper was a member of the Legal Service of the Commission of the European Communities (1979-1884, 1987-1999 and 2002-2007) where he was active in the 'Competition' and 'External Relations' teams. He was Legal Advisor to the Commission's 'Uruguay Round Negotiation' team and later combined this with heading a newly formed GATT/WTO litigation group formed within the Commission's Legal Service (1991-1996). From 1996 to 1999 he worked in the team in charge of freedom of movement of persons, social affairs and Justice & Home Affairs. From 1999 to 2002 he was Director of the Legal Affairs Division of the secretariat of the World Trade Organization (WTO).

He acted as agent of the European Commission before the European Court of Justice (ECJ) and the Court of First Instance of the European Communities (CFI) in cases concerning competition, the internal market, freedom of movement of persons, and the trade- and external relations powers of the Community.