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This article deals with the performance analysis of orthogonal frequency division multiplexing (OFDM) amplify-and-forward (AF) relay system with subcarrier mapping (SCM) in the presence of carrier frequency offset (CFO). Although SCM in an OFDM system has been investigated extensively, nevertheless, the bit error rate (BER) of the system with CFO is not yet available in the literature. This paper presents the BER analysis of a dual hop OFDM AF relay system with ordered subcarrier paring schemes, i.e., best-to-worst (BTW) SCM and best-to-best (BTB) SCM. Accurate close-form expressions are derived for end-to-end BER while considering a dual-hop fixed gain AF relaying system with CFO in Rayleigh fading channel. To provide more insights, their closed-form asymptotic expressions are then obtained. It is shown that the presence of CFO causes the BER of system maintain a fixed level even while signal-to noise ratio (SNR) is in high regime. The simulation results verify that the derived average BER expressions are accurate in Rayleigh fading channel.