An apparatus and a method for estimating a channel in a Broadband Wireless Access (BWA) communication system are provided. The apparatus includes a subcarrier demapper for extracting pilot symbols at preset positions for a channel estimation; and a channel estimator for acquiring channel estimate values of subcarriers through an Infinite Impulse Response (IIR) filtering using the pilot symbols provided from the subcarrier demapper and a preset filter factor. Thus, the channel condition can be estimated by taking into account the channel change.