The cerebellum has recently been recognized for its role in non-motor functions, including classical fear conditioning. However, the molecular mechanisms underlying non-motor learning and memory remain largely unknown. Here, we investigate the transcriptional changes in the cerebellum associated with auditory fear conditioning. Spatial transcriptomic analysis revealed that in the deep cerebellar nuclei (DCN), an output region of the cerebellum, the expression of immediate early genes increased following fear learning and retrieval, suggesting that DCN may contribute to fear memory processing. As for the cerebellar cortex, robust and region-specific transcriptional changes were observed, with distinct expression patterns emerging across the Purkinje cell layer of vermis region. To further elucidate transcriptional changes in specific DCN cell types involved in fear processing, we performed single-nucleus RNA sequencing and identified prominent gene expression changes in + inhibitory neurons. Collectively, our findings highlight region- and cell-type-specific molecular adaptations in the cerebellum, providing insights into its contribution to non-motor learning.