Self-encoded spread spectrum (SESS) is a novel modulation technique that acquires its spreading sequence from the random input data stream rather than using the traditional pseudo-random-code generators. It has been shown that the memory in SESS can improve the system performance significantly in fading channel. In this study the authors analyse the tracking error of SESS system in the presence of multipath Rayleigh fading channels. Code Shuffling is introduced to randomise the spreading code, which in turn mitigates the effect of reflected path component and enhances the accuracy and performance of iterative detection (ID) against multipath effects. The performance comparison of SESS with C/A code is investigated with the main focus on short multipath delay scenarios. The results demonstrate that ID can significantly mitigate the pseudorange multipath error without any bandwidth expansion.