Objective To observe the changes of the acetylation of lysine 9 on histone H3 (H3K9) and H3K14 in the different brain regions during rapid eye movement after sleep deprivation (SD) in rats. Methods Modified multiple platform was used to establish the SD model. Forty-eight rats were randomly divided into four groups: control group, one day post-SD group (SD1), three day post-SD group (SD3) and six day post-SD group (SD6). Western blotting was performed to examine the changes in the acetylation levels of H3K9 and H3K14 in different brain regions, including hippocampus, hypothalamus, prefrontal cortex and raphe nucleus. Results Compared with the control group, in the SD1, SD3, and SD6 groups, the acetylation levels of H3K9 and H3K14 in the hippocampus and hypothalamus significantly decreased time-dependently. In contrast, their levels in the ventromedial prefrontal cortex and raphe nucleus markedly increased in the SD6 but not in the SD1 and SD3 groups. Conclusion The increase of H3K9 and H3K14 acetylation in the hippocampus and hypothalamus as well as the decrease of H3K9 and H3K14 acetylation in the prefrontal cortex and raphe nucleus may be involved in the development of sleep disorders.