Frequency hopping spread spectrum (FHSS) communication systems offer significant performance advantages in view of their low probability of intercept, improved performance in multipath fading environments and their ability to avoid interference by hopping into low interference frequency channels. For the transmitted sequence to be correctly received and demodulated, the frequency hop sequence used at the receiver should be similar to that employed in the transmitter. Code acquisition in frequency hopping attempts to address this problem by providing a frequency hop pattern at the receiver that is nearly identical to that used at the transmitter. Code acquisition brings the alignment between the transmitter and the receiver hop pattern to at least one hop period. In this paper, the serial search code acquisition, which is the first step of synchronization, is studied for frequency hopping spread spectrum (HFSS) system over Rayleigh fading channel. Simulation results show the effect of fading channel on the code acquisition.