Despite earning back-to-back nominations for the prestigious prize, the 24-year-old is once again a shock omission from the final three shortlist.
Kerr was beaten out by Germany captain Dzsenifer Marozsan, Norway striker Ada Hegerberg and Brazil great Marta.
The awards are based on coaches and players' respective achievements during the period from 7 August 2017 to 24 May 2018 inclusive.
The results are compiled by a panel of experts representing all of FIFA’s confederations including national team coaches, team captains, journalists and fans.
During the award voting period Kerr scored 33 goals in 34 games for both club and country as well as breaking the record for most goals in an NWSL season with 17.
She was also named AFC Women's Player of the Year, Julie Dolan medal winner, PFA Women's Player of the Year, Golden Boot winner in the NWSL and W-League as well as Young Australian of the Year.
All award winners will be revealed at The Best FIFA Football Awards show in London on September 24.
