In recent years, it has become clear that non-coding RNAs play an important role in regulating the development of various organs and pathological conditions, including cerebral ischemia and reperfusion. Non-coding RNAs are mainly represented by long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs). Most of the human genome is transcribed into such RNAs. Excessive activation of autophagy during cerebral ischemia and reperfusion results in autophagic neuronal death in addition to apoptotic death. This review shows that regulation occurs via the lncRNA (or circRNA)/miRNA/target protein signaling axes. A knockdown or a decrease in lncRNA level can lead to a significant increase in miRNA levels, followed by a decrease in the levels of messenger RNA (mRNA) of autophagy-related protein (ATG) and ATG protein itself. This leads to inhibition of autophagy and alleviation of brain ischemia-reperfusion injury. Changes in miRNA and mRNA levels of the target protein occur due to the presence of complementary nucleotide sequences with lncRNA and miRNA, respectively. If the target protein is not an ATG protein, neuroprotection during cerebral ischemia and reperfusion can result from both inhibition and activation of autophagy. The further study of the regulatory role of non-coding RNAs is important as it may help to counteract the effects of excessive autophagy activation and other adverse effects of ischemia-reperfusion injury.