A method and apparatus for applying autonomous denial in a wireless communication system is provided. A user equipment (UE) counts the number of aggregated denials of uplink (UL) subframes in all serving cells or each serving cell over a validity period including previous subframes and a current subframe. If the number of aggregated denials of UL subframes in all serving cells or each serving cell is less than a threshold, the UE is allowed to deny scheduled UL transmission at the current subframe.