Flanagan turned professional in 2004 and after winning a Von Nida Tour event in Queensland he eventually found his way onto the then Nationwide Tour where, in 2007 he won three events and graduated to the PGA Tour through the Battlefield Promotion and was named Nationwide Tour Player of the Year.
Despite a good start to his rookie season on the PGA Tour he failed to retain his status and was back on the secondary tour in 2009. His only other win would come three years later when winning the 2012 BMW Charity Pro Am on the Nationwide Tour defeating fellow countryman Cameron Percy in a playoff for that title.
Flanagan plays the PGA Tour of Australasia where he finished 19th on the 2018 Order of Merit including a best of 6th place at the Australian PGA Championship
