Ultrasonic imaging using complementary coded pulses offers the SNR improvements of signal coding without the filter side-lobes introduced by single transmit codes. The effects of the transducer and motion in the medium, however, can introduce mismatch artefacts and high side-lobes due to misalignment. A method for filtering and motion compensation of complementary coded signals appropriate for use in medical imaging scenarios is presented in this paper. The method has been shown by simulation to reduce side-lobes to levels that compare favourably to systems using FM-coded signals of similar length and bandwidth while increasing coding gain and range resolution.