EPI has been widely used for fMRI due to its relatively fast imaging speed. However, as one of its drawbacks, ghost artefacts need to be corrected. In the community, an approach that utilises three non-phase encoded navigator echoes is commonly used for the correction. Although this scheme is quite effective, as the matrix size increases for high-resolution imaging the navigator echoes constitute a significant contribution in increasing the minimum required TE. To overcome this issue, this work employs an alternative navigator echo scheme. Here, its performance was analysed and whole-brain submillimetre-resolution fMRI (0.75 × 0.75 mm2) was demonstrated at 3T.