An apparatus for performing a scan procedure according to an orthogonal frequency division multiple access (OFDMA) signal and a mobile station comprising the same are provided. The characteristic of the apparatus is that it comprises two FIT input buffers. In a first period of a downlink subframe, the first FFT input buffer is used for data transmission. In a second period of the downlink subframe, the second FFT input buffer is used for storing more than one OFDMA sample in advance for further processing. In a third period of an uplink subframe, the stored OFDMA samples can be used to generate a refined frame boundary and calculates a CINR value of each of a plurality of neighboring base stations. Therefore, the apparatus and the MS can perform the scan procedure without downgrading the network efficiency.