In September 2008 he was called up to the Northern Ireland under-17 squad.
He was a part of the under-19s run to the Milk Cup final in 2010. On 27 July he scored a vital equalizer against Mexico at the Coleraine Showgrounds, which helped take the team above Mexico on goal difference in the final table.
In August 2010, he received his first call-up the under-21 squad, and he played for the Northern Ireland national under-21 football team in a 2011 UEFA European Under-21 Football Championship qualification match against Germany on 7 September 2010. He was called up to the senior Northern Ireland team for the first time in February 2011. He made his debut on 9 February 2011, as a 66th-minute substitute in Northern Ireland's 3–0 defeat to Scotland in the 2011 Nations Cup. Scotland did not score while Thompson was on the field.