Due to his increased playing time domestically with Toulouse, Sissoko missed the 2007 edition of the Sendai Cup in Japan and numerous other under-19 tournaments and only featured in 2008 UEFA U-19 Championship qualification matches. He made his debut on 28 October 2007 in a 5–0 rout of Luxembourg in the first qualifying round. Similar to the competition at under-17 level, France were later eliminated in the Elite Round portion of the competition. Sissoko earned his first call up to the under-21 team for their friendly match against Bosnia and Herzegovina on 9 September 2008. He subsequently made his debut in the match, which France won 1–0. Sissoko scored his only goal with the team on 31 March 2009 in the team's 2–0 win over England at the City Ground in Nottingham. He featured with the team frequently as they were attempting to qualify for the 2011 UEFA European Under-21 Football Championship. The team's ultimate failure to qualify for the competition effectively ended Sissoko's under-21 career, though he still appeared in friendly matches against Turkey, Denmark, and Russia in 2010 as he was still eligible to participate in non-competitive matches.