Fraser Brown has represented Scotland at many levels. He debuted for the Scotland Under 18s in 2007. In 2008, he was selected for the Scotland under-20s squad for the 2008 under-20s Six Nations, playing all five rounds. He was announced as captain for the 2009 season, and led the Scots to an 18–17 victory over Wales in the opening round of the 2009 under-20s Six Nations. He continued as captain going into the 2009 IRB Junior World Championship, the side eventually finishing ninth.