A method and apparatus of performing channel estimation in a wireless communication system are provided. The method includes determining a channel response value of a midamble sequence included in a downlink slot, detecting a first channel response value of a window allocated to a user and a second channel response value of a window allocated to at least one other user based on the channel response value of the midamble sequence, determining whether a Base Station (BS) of a current cell uses beamforming based on the first and second channel response values, and combining the first and second channel response values and using the combined channel response value for signal detection if it is determined that the BS does not use beamforming.