MicroRNAs are involved in the regulation of various cellular processes, including cell apoptosis and autophagy. Expression of microRNA-99a (miR-99a) is reduced in apoptotic neonatal mice ventricular myocytes (NMVMs) subjected to hypoxia. We hypothesize that miR-99a might restore cardiac function after myocardial infarction (MI) by up-regulation of myocyte autophagy and apoptosis. We observed down-regulated miR-99a expression in NMVMs exposed to hypoxia using TaqMan quantitative reverse transcriptase-polymerase chain reaction analysis (RT-PCR). We also observed that miR-99a overexpression decreased hypoxia-mediated apoptosis in cultured NMVMs. To investigate whether overexpression of miR-99a in vivo could improve cardiac function in ischaemic heart, adult C57/BL6 mice undergoing MI were randomized into two groups and were intra-myocardially injected with lenti-99a-green fluorescent protein (GFP) or lenti-GFP (control). Four weeks after MI, lenti-99a-GFP group showed significant improvement in both left ventricular (LV) function and survival ratio, as compared to the lenti-GFP group. Histological analysis, western blotting analysis and electron microscopy revealed decreased cellular apoptosis and increased autophagy in cardiomyocytes of lenti-99a-GFP group. Furthermore, western blotting analysis showed inhibited mammalian target of rapamycin (mTOR) expression in the border zones of hearts in miR-99a-treated group. Our results demonstrate that miR-99a overexpression improves both cardiac function and survival ratio in a murine model of MI by preventing cell apoptosis and increasing autophagy via an mTOR/P70/S6K signalling pathway. These findings suggest that miR-99a plays a cardioprotective role in post-infarction LV remodelling and increased expression of miR-99a may have a therapeutic potential in ischaemic heart disease.