The single-carrier frequency division multiple access (SC-FDMA) system is a popular system in mobile communication because of its advantage of low peak-to-average-power-ratio (PAPR), and the use of frequency-domain equalizers to reduce inter-symbol interference (ISI) and inter-carrier interference (ICI). This paper presents a comprehensive study of the SC-FDMA system with PAPR reduction using clipping and filtering in the presence of channel estimation errors for two different versions of SC-FDMA adopting the FFT and the DCT. The effect of peak power reduction and the channel estimation error on the system bit error rate (BER) is investigated. Simulation results prove that the BER performance is not much affected by the PAPR reduction.