Ischemia–reperfusion (IR) injury is a serious concern in the treatment of coronary heart disease. Recently, aerobic glycolysis has shown potential benefits against IR injury. Scutellarin (Scu), a flavonoid found in Erigeron breviscapus has multiple potentially cardio-protective properties. In this study, we used hypoxia/reoxygenation (H/R) injury to mimic IR injury in vitro. First, we evaluated the protective effects of Scu against HR in H9c2 cells, which included inflammation damage, apoptosis injury and oxidative stress. Then, we verified the effects of Scu on Warburg effect in H9c2 cells under HR injury. The results indicated that Scu increased aerobic glycolysis by reducing pH, increasing lac, enhancing phosphofructokinase (PFK) activity, and elevating p-PKM2/PKM2 levels. Next, we built a panel of six lncRNAs and seventeen miRNAs that were reported to mediate the Warburg effect. Based on the results, miR-34c-5p was selected as the entry point for further experiments. Then, we found Scu could alleviate HR-induced elevation of miR-34c-5p. Up-regulation of miR-34c-5p could weaken the protective effects of Scu in cell viability, inflammatory damage and oxidative stress. The facilitation of Warburg effect by Scu was also reversed by miR-34c-5p mimic in H9c2 cells. Next, we found the mRNA and protein of ALDOA were reduced after HR injury, and these could be reversed by Scu. Downregulation of ALDOA or Mimic of miR-34c-5p could reduce the effects of Scu that maintained mRNA and protein levels of ALDOA. SiRNA of ALDOA could decrease anti-HR effects of Scu in H9c2 cell. Summarily, our study demonstrated that Scu provides cardio-protective effects against IR-induced myocardial cell injury by upregulating Warburg effect via miR-34c-5p/ALDOA pathway in H9c2 cell model.