Experimental evidence in animal models indicates that the brainstem plays a major role in sensory modulation. However, mapping functional activity within the human brainstem presents many methodological challenges. These constraints have deterred essential research into human sensory brainstem processing. Here, using a 3T functional Magnetic Resonance Imaging (fMRI) sequence optimised for the brainstem, combined with uni- and multivariate analysis approaches, we investigated the extent to which functional activity of neighbouring somatosensory nuclei can be delineated in the brainstem, thalamus, and primary somatosensory cortex (S1). Whilst traditional univariate approaches offered limited differentiation between adjacent hand and face activation in the brainstem, multivariate classification enabled above-chance decoding of these activity patterns across S1, the thalamus, and the brainstem. Our findings establish a robust methodological approach to explore signal processing within the brainstem and across the entire somatosensory stream. This is a fundamental step towards broadening our understanding of somatosensory processing within humans and determining what changes in sensory integration may occur in clinical populations following sensory deprivation.