The key clinical symptoms and previous findings of RA show a circadian variation, with more prominent joint swelling, stiffness, and pain occurring in the early morning. Moxibustion is able to relieve RA in various pass ways, however, there is no verifying study results for the pathological rhythm of RA. Therefore, we conducted this work to verify whether moxibustion could adjust RA circadian rhythm according to regulate core clock genes. Based on these previous findings that circadian timekeeping is disturbed in RA at molecular level, the aim of this study was to observe the influence of moxibustion on expression level and circadian rhythm of REV-ERBα at different tissues of RA rats. Furthermore, the expression level of core clock genes closely related to RA were evaluated by RT-PCR. 96 SD rats were randomly assigned as 1:1:1:1 ratio to 4 groups for normal control group, RA model group, 5-7 am moxibustion group, and 5-7 pm moxibustion group. RT-PCR was used to measure the relatively expression quantity of REV-ERBα, CLOCK, BMAL1, and PER2 in hypothalamus, hippocampus, and adrenal gland. In RA rats, the expression level of REV-ERBα mRNA were up-regulated in different tissues, and moxibustion potentially up-regulated them in different degrees. In untreated RA rats, the circadian rhythm of REV-ERBα mRNA in hippocampus and adrenal gland both disappeared (P>0.05) and moxibustion was able to recover them (P<0.05). The expression level of CLOCK and PER2 mRNA in hippocampus and adrenal gland were down-regulated significantly (P<0.05) in RA model rats, while moxibustion up-regulated both of them in hippocampus (P<0.05). These results suggested together that moxibustion can benign regulate circadian rhythm of REV-ERBα in different tissues of RA rats. It was revealed that moxibustion not only recovered the losing diurnal oscillation of REV-ERBα in hippocampus and adrenal gland, but also adjusted the circadian rhythm of REV-ERBα in hypothalamus, hippocampus, and adrenal gland to close the normal circadian pattern.