In this study we described the seasonal profile of the actin and Cdk5 levels in different brain structures of Yakut long-tailed ground squirrels (Spermophilus undulatus) during their annual cycle. Experiments were performed with adult Yakut ground squirrels, both male and female, weighing 600–800 g (n = 35) at different stages of their annual cycle, viz., in the summer, the period of the maximum activity of the animals; in the autumn, during preparation for hibernation; in the winter, during hibernation; in the spring, at the exit of the animals from the hibernating state. Our results indicate that actin mRNA increased by 1.9 times (p = 0.0001) in the frontal cortex, the hippocampus, and the caudal brainstem during hibernation. In the brainstem, a significant increase in actin mRNA started to develop in autumn, in normothermic animals at the stage of their preparation for hibernation (p = 0.0078). At the exit of animals from the torpid state, the level of hippocampal expression decreased significantly by 4.5 times; in the cortex and brainstem it decreased to the level of summer animals. In contrast, the dynamics in the cerebellum had opposite direction: actin mRNA level decreased significantly during the preparation for hibernation (p = 0.037), remained low in torpid animals (p = 0.051), and increased after awakening. The changes in the total protein level were observed only in the hippocampus, along with increased expression of Cdk5 mRNA during hibernation (p = 0.003) and at the exit from it (p = 0.001). Detected differences in the seasonal metabolic profile of cytoskeleton proteins in the hippocampus of Yakut long-tailed ground squirrels support a substantial structural plasticity of this brain structure during the hibernation cycle that was described previously in morphological and biochemical studies.