<p>Spontaneous daily torpor in the Djungarian hamster is a precisely timed energy-saving strategy that occurs in winter to withstand challenging conditions. It features a transient but pronounced decrease in metabolic rate, body temperature and other physiological parameters. The hypothalamus is thought to remain active to coordinate torpor, but there is limited data with sufficient anatomical resolution to identify nucleus-specific regulatory mechanisms. This study sought to pinpoint hypothalamic regions involved in torpor control and characterize their transcriptional activity using nucleus-specific RNA sequencing. Hamsters were acclimated to short photoperiod and sampled at defined torpor phases (entry, nadir, arousal, post-torpor) and matched times on a torpor-free day. To identify transcriptionally active regions, radioactive in situ hybridization of <i>c-Fos</i> was performed. Among all examined nuclei, only the suprachiasmatic nucleus (SCN), the master circadian clock, showed increased <i>c-Fos</i> expression during torpor nadir and arousal compared with time-matched normotherms. To assess functional involvement, SCN and paraventricular nucleus (PVN) as key SCN output target, were isolated via laser-capture microdissection from additional animals during torpor entry and arousal for mRNA sequencing. The SCN displayed robust, torpor-specific transcriptional regulation, underscoring its central role in timing daily torpor. The PVN showed fewer but potentially meaningful alterations, including altered expression of aromatase. Enhanced mitochondrial and clock gene activity in the SCN suggests preserved function during hypometabolism, while phase-dependent transcriptional suppression in both nuclei reflects distinct entry–arousal dynamics. Together, these results identify the SCN as a primary coordinator of torpor, with SCN–PVN signalling highlighted as a key pathway for future investigation.</p>