Hypoxia inducible factor 1α (HIF‑1α) has been reported to play a key role in protecting neurons from ischaemic injury. However, the exact molecular mechanisms remain largely unclear. PC12 cells were exposed to oxygen glucose deprivation/reoxygenation (OGD/R) conditions to mimic ischaemic injury in vitro. The expression of the HIF‑1α mRNA, miR‑20a‑5p, and kinesin family member 5A (KIF5A) mRNA was tested using qRT-PCR. Levels of the HIF‑1α, LC3I/II, P62, LAMP2, cathepsin B (CTSB) and KIF5A proteins were determined using western blotting. The CCK‑8 assay was conducted to assess PC12 cell viability. DQ‑Red‑BSA and LysoSensor Green DND‑189 dyes were employed to measure the proteolytic activity and pH of lysosomes, respectively. The interaction between miR‑20a‑5p and HIF‑1α or KIF5A was verified by performing chromatin immunoprecipitation (ChIP) and/or dual‑luciferase reporter assays. TUNEL staining was adopted to assess PC12 cell death. GFP‑LC3 and RFP‑GFP‑LC3 probes were used to examine the autophagy status and autophagy flux of PC12 cells. A rat middle cerebral artery occlusion‑reperfusion (MCAO/R) model was established to investigate the role of the HIF‑1α/miR‑20a‑5p/KIF5A axis in ischaemic stroke in vivo. OGD/R exposure initiated PC12 cell autophagy and injury. HIF‑1α expression was substantially increased in PC12 cells after OGD/R exposure. Overexpression of HIF‑1α reversed the effects of OGD/R on reducing cell viability, blocking autophagy flux and inducing lysosome dysfunction. These rescue effects of HIF‑1α depended on KIF5A. HIF‑1α negatively regulated miR‑20a‑5p expression by targeting its promoter region, and miR‑20a‑5p directly targeted and negatively regulated the KIF5A mRNA. Overexpression of miR‑20a‑5p abolished the effects of HIF‑1α on rescuing OGD/R‑induced injury in PC12 cells. The effects of the HIF‑1α/miR‑20a‑5p/KIF5A axis were verified in MCAO/R rats. HIF‑1α protects PC12 cells from OGD/R‑induced cell injury by regulating autophagy flux through the miR‑20a‑5p/KIF5A axis.