Wheater has represented England at under-16, under-17, under-18, under-19 and most recently under-21 level. He played at the 2004 U17 European Championships and earned his debut under-21 call-up in August 2007 along with the uncapped Adam Johnson after impressing while on loan at Darlington. He was a regular in the 2009 U21 European Championship qualifying. In October 2008 he scored the equaliser against Wales in the first leg of the play-offs and England went on to win 3–2 and 5–4 on aggregate to qualify. He was supposed to be in the squad for the tournament but withdrew after sustaining an injury.