2D EPI-based Quantitative Susceptibility Mapping offers a means to localise brainstem structures very quickly. However, this comes at the price of limited achievable slice thickness, restricting the precision of the localisation. In this work, we develop a fast super-resolution reconstruction method for complex MRI data, allowing the reconstruction of high resolution magnitude and phase images, and hence also high resolution susceptibility maps. We demonstrate that the reconstructed super-resolution 2D EPI images significantly improve the visibility of small structures allowing for improved localisation of the brainstem and other small structures such as veins in the generated susceptibility maps.