Multi-echo gradient echo (mGRE) sequences have been widely adapted in clinical and scientific practice for different purposes to their capability of performing Dixon MRI, generating multi-contrast images and extracting multi-parametric maps. This work aims to extend mGRE-based techniques for imaging whole head, where further technical developments are required due to the co-existence of fat and large B0 inhomogeneity in regions such as the skull base and neck. Specifically, bipolar mGRE data were acquired with a single sequence that contains both a short echo-spacing (ΔTE) echo train to capture water-fat and B0 phase shifts (for proton density fat-fraction (FF) and B0 mapping) and a longer ΔTE echo train (and long echo times) to capture subtle susceptibility variations and R2* information. The mGRE images covering the whole head (spatial resolution 1.0 × 1.0 × 2.0 mm3) were acquired in 5 min. An automated processing pipeline was implemented to use the FF and B0 maps determined from the short-TE train to compensate for the effects of fat, remove the background phase for whole-head quantitative susceptibility mapping, and reduce the difficulty of spatial phase unwrapping of the long echo-time data. Data from healthy volunteers imaged on a 3 T scanner along with phantom validation are presented. Co-registered quantitative multi-parametric maps (FF, B0 inhomogeneity, R2*, local frequency shift and quantitative susceptibility) and multi-contrast images covering the whole head were successfully generated in processing times of several minutes.