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The cerebellum plays an important role in human brain development. To improve the spatial specificity of the analysis of human cerebellar magnetic resonance imaging (MRI) data, we present a new template of the neonatal human cerebellum and brainstem based on the anatomy of 20 full-term healthy neonates. The template is spatially unbiased, which means that the location of each structure is not biased by the anatomy of the individuals used to create the template. In comparison to current whole-brain templates, it allows for an improved voxel-by-voxel normalization for MRI analysis. To align the cerebellum to the template, it needs to be isolated from the surrounding tissue, a process for which an automated algorithm has been developed. Our methodology outperforms normalization to a whole-brain neonatal template, using either linear or nonlinear transformations. Our algorithm reduces the spatial variability of the infratentorial area, while simultaneously increasing the overlap of the cerebellum. The template and the related software are freely available as part of SUIT v3.3 SPM toolbox.