Long non-coding RNAs (lncRNA) and circular RNAs (circRNA) that sponge miRNAs could indirectly regulate gene expression, contributing to certain biological processes. This study aimed to investigate the role of non-coding RNAs in the pathogenesis of myocardial ischemia reperfusion-injury (MIRI). MIRI in male C57B/6J mice was induced by left anterior descending coronary artery ligation occlusion for 30 min, and 4 h of reperfusion. RNA sequencing was performed to obtain the mRNA and non-coding RNA expression profiles of the MIRI and sham groups. Bioinformatic methods were used to analyze the co-expression RNAs, miRNA binding sites and competitive endogenous RNA (ceRNA) pairs. Differentially expressed RNAs were identified with a cutoff fold change > 2 and p < 0.05. A total of 64 mRNAs were upregulated and 98 mRNAs were downregulated, and 10 lncRNAs were upregulated and 10 lncRNAs were downregulated. All altered (p < 0.05) mRNAs were selected for gene ontology and pathway analysis. The AMP-activated protein kinase (AMPK) signaling pathway was enriched in the downregulated genes, and the activation of AMPK was confirmed by western blotting. The lncRNA co-expression network and ceRNA network base on genes in AMPK signaling pathway were then constructed, revealing that ENSMUST00000147762.7 and TUCP_000184 might be key regulators in MIRI induced AMPK activation. The expression levels of AMPK signaling-related RNAs and those involved in the ceRNA network were validated using qRT-PCR. Overall, this study identified potential new targets on AMPK signaling in MIRI.