In this paper, cyclic prefix based time synchronization and comb type channel estimation are studied for a SC-FDMA systems with AF relaying cooperative communication technique over time varying channels. Preamble based synchronization and its usage in the block type channel estimation for SC-FDMA systems are vulnerable to time varying channels. Therefore, undeductible channel estimation errors in time varying channels limit the performance of SC-FDMA systems. For this reason, in this paper comb type channel estimation is proposed to track the channel variations. Simulation results demonstrate that the cyclic prefix based time synchronization and comb type channel estimation have better bit error rate performance over time varying channels.