In 1986 Supachai Panitchpakdi was appointed as Deputy Minister of Finance, but when the parliament was dissolved in 1988 he left politics and became president of the Thai Military Bank. In 1992 he returned to politics and became Deputy Prime Minister until 1995, responsible for trade and economics. During the Asian financial crisis in November 1997 he returned to be Deputy Prime Minister and also became Minister of Commerce.
In September 1999 he was elected to become director-general of the World Trade Organization (WTO), taking office on September 1, 2002.