An apparatus and method for power distribution by Frequency Allocation (FA) in a multi-band broadband wireless communication system are provided. The method includes detecting at least one of a loading value and a performance efficiency value by band, calculating a power distribution value by band using the detected value and calculating a power value by band using the calculated band power distribution value. The method and apparatus provide a scheme that can vary a power distribution of each band according to need and cope with subscriber capacity more flexibly when a plurality of diverse systems coexist.