Hong Kong League XI
Thompson has been capped for Scotland at under-21 level and won his first full Scotland cap against France in March 2002 and got his first start a month later, scoring his first goal in May 2002 against a Hong Kong League XI during the HKSAR Reunification Cup. He would score twice more for his country, in a 3–1 friendly win over Canada at Easter Road in October 2002 and equalizing in a 1–1 draw away to Moldova in a World Cup qualifier in October 2004.