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Sparse frequency agile orthogonal frequency division multiplexing (SFA-OFDM) signal brings excellent performance to electronic counter-countermeasures (ECCM) and reduces the complexity of the radar system. However, frequency agility makes coherent processing a much more challenging task for the radar, which leads to the discontinuity of the echo phase in a coherent processing interval (CPI), so the fast Fourier transform (FFT)-based method is no longer a valid way to complete the coherent integration. To overcome this problem, we proposed a novel scheme to estimate both super-resolution range and velocity. The subcarriers of each pulse are firstly synthesized in time domain. Then, the range and velocity estimations for the SFA-OFDM radar are regarded as the parameter estimations of a linear array. Finally, both the super-resolution range and velocity are obtained by exploiting the multiple signal classification (MUSIC) algorithm. Simulation results are provided to demonstrate the effectiveness of the proposed method.