A method and apparatus for handling frequency priorities inherited from other radio access technologies (RATs) in a wireless communication system is provided. A user equipment (UE), which inherits information on dedicated frequency priorities from other RATs, applies the dedicated frequency priorities while a timer is running. However, upon receiving information on a broadcast frequency priority from a current cell, and when the information on the broadcast frequency priority includes priority information of a RAT of which priority information is not included in the information on the dedicated frequency priorities, the UE stops applying the dedicated frequency priorities and applying the broadcast frequency priority.