Background: Nowadays, obesity can affect heart function and induced atherosclerosis, high blood pressure, and heart arrhythmia, which has become a major problem for global health. Objectives: The present study aimed to review the effect of six weeks of high-intensity interval training (HIIT) on gene expression levels of PGC-1α and eNOS in the heart tissue of obese male rats. Methods: In this experimental study, 14 high-fat diet (HFD)-induced obese rats were divided into two groups of control and training. Also, 7 rats were placed in a non-obese control group to investigate the effects of obesity on research variables. During six weeks, rats in the training group performed HIIT three days per week. After six weeks, all rats were sacrificed, and their heart tissue was removed to measure the PGC-1α and eNOS gene expression. We used one-way ANOVA with Tukey’s post hoc tests (P ≤ 0.05) for statistical analysis. Results: HFD significantly decreased PGC-1α (P = 0.04) and eNOS (P = 0.001) gene expression, but HIIT significantly increased PGC-1α (P = 001) and eNOS (P = 0.001) gene expression. Conclusions: HIIT seems to improve cardiac gene expression levels of PGC-1α and eNOS of male obese rats.