The Brainstem Navigator toolkit is a collection of in-vivo brainstem nuclei atlas labels, MRI templates and documentation. The atlas is in stereotactic space and includes gray matter brainstem regions involved in arousal/sleep, autonomic, motor, sensory and limbic function. The atlas labels of brainstem nuclei were created by semi-automatic and manual segmentations of multi-contrast MRI of living humans at 7 Tesla. This toolkit includes a tutorial of scripts with alignment routines of the brainstem nuclei atlas labels to structural, diffusion and functional MRI data of individual subjects. This package has been made available to enable researchers to identify the location of brainstem nuclei in both conventional and advanced MRI (e.g. 3 Tesla, 7 Tesla).