Having had various trial periods with clubs such as Manchester United, Fiorentina and Chelsea, and with his Brøndby contract expiring in December 2009, Boilesen agreed a move to the Netherlands, with Ajax paying Brøndby 4 million DKK in compensation (roughly €500,000). Followed by a number of top European clubs, Boilesen chose Ajax on advice from fellow Danish youth international and Ajax player Christian Eriksen. Signing a 4-year contract, binding him to the club until the Summer of 2013, he initially joined the youth ranks where his first season with Ajax was stalled by injuries. Once recovered he solidified a starting position for Ajax A1, the clubs' under-19 team, and even made appearances for the reserves team willy Jong Ajax.