Wilkshire has played eighty times for the Australian national team. This includes matches at both the 2006 and 2010 FIFA World Cups, as well as the 2007 and 2011 AFC Asian Cups. He was also a member of the squad at the 2005 FIFA Confederations Cup. Previously, with Australia's youth sides, Wilkshire took part in the 2001 FIFA U-20 World Cup and the 2004 Summer Olympics.