Nike largely attributed the shift to geographical differences, claiming it was too difficult to run its business from Melbourne while its agency was based in Sydney. The workload has also diminished, making the relationship less feasible.
Nike Australia marketing director, Carl Grebert, said the change was not a reflection on FCB's abilities.
"The relationship with FCB Sydney has produced outstanding work for a brand which is constantly in the spotlight and which carries an enormous burden of expectations, Grebert said.
"The work for the 2000 Olympic Games in particular was recognised as world class.
"However, while a long distance relationship was viable with the nature of our previous work, we've decided that a more local relationship will better suit our current needs."
Nike is renowned for cutting edge creative work.
Earlier this year, the brand won the Grand Prix award at the Cannes International Advertising Festival for a 'Tag' commercial created by Wieden & Kennedy Portland.
Locally, Nike has already drawn a shortlist of new candidates, although their identities remain cloaked.
