The effect of intermittent food restriction (IFR) on the Central Nervous System is unclear, especially when alternated with an obesity-inducing diet (DIO). This study aimed to evaluate key genes involved in energy-regulation imbalance in the hypothalamus after IFR and DIO alternation. Therefore, 45-d-old female Wistar rats were divided into 4 groups: standard control (ST-C), fed with an ad libitum standard diet; DIO control (DIO-C), fed with a DIO in the first and last 15 d of the intervention and a standard diet between the 16th and 45th day; standard restricted (ST-R), fed with a standard diet in the first and last 15 d of the intervention followed by IFR at 50% of the ST-C diet between the 16th and 45th day; and DIO restricted (DIO-R), fed with a DIO in the first and last 15 d of the intervention and subjected to IFR under the same conditions as the ST-R group. At 105 d of age, animals were euthanized, and the hypothalamus was removed for quantitative polymerase chain reaction analysis. The ST-R and DIO-R groups showed higher inhibitor of nuclear factor kappa-B kinase subunit beta (P < 0.001; P = 0.029) and nuclear factor kappa B (P < 0.001; P = 0.029) gene expression when compared with the ST-C group. The same held true for the JNK (P = 0.001; P = 0.003) and PPARα genes (both P < 0.001). Instead, the DIO-R group exhibited higher CCL5 gene expression than the ST-C (P = 0.001) and DIO-C (P < 0.001) groups, whereas all groups had higher SOCS3 gene expression than did the ST-C group. These data together suggest that IFR, whether combined with DIO or not, alters the expression of critical genes involved in energy regulation imbalance in the hypothalamus, which warrants caution and more research, because long-term usage might be hazardous.