In 1994 North York councillor Barry Burton died of cancer and the North York city council appointed Minnan-Wong as interim councillor for Ward 12. He was subsequently elected to the position in the November 1994 municipal election. In 1997 he was elected as one of two councillors representing Ward 11 – Don Parkway to the city council of the new amalgamated city of Toronto. In July 2022 Minnan Wong announced he would not seek re-election in the October 2022 municipal election after 28 years in elected office.
