To date, our understanding of the relationship between middle cerebral artery occlusion/reperfusion (MCAO/R)-induced ischemia stroke and circular RNAs (circRNAs) remains limited. The objective of this research was to explore the roles and underlying mechanisms of the circDnajc1/miR-27a-5p/C1qc signaling pathway in the development of ischemia stroke. For in vitro experiments, an oxygen-glucose deprivation/reperfusion (OGD/R) cell model was established following neuron-microglia co-culture. circDnajc1 siRNA and pcDNA3.1-circDnajc1 overexpression vectors were constructed and transfected into primary microglia. For in vivo experiments, an MCAO/R rat model was established. The molecular mechanisms were investigated using flow cytometry, RT-qPCR, immunofluorescence, RNA immunoprecipitation, and luciferase reporter gene assays. In vitro experiments showed that circDnajc1-induced cellular activation following microglia OGD/R injury, promoted the release of inflammatory factors, downregulated miR-27a-5p, upregulated C1qc, C3, and C5ar, and promotes neuronal apoptosis after microglia OGD/R injury. Interference with circDnajc1 reversed these effects. In vivo experiments, circDnajc1 knockdown exerted a protective effect on neurons in MCAO/R rats and inhibited microglial activation and the release of inflammatory factors. Consistent with the in vitro experiments, circDnajc1 regulated on the expression of downstream target genes of miR-27a-5p, C1qc, C3, and C5ar. CircDnajc1 plays a critical role in ischemia stroke and may influence nervous system homeostasis by regulating the circDnajc1/miR-27a-5p/C1qc signaling axis, which promotes microglia activation and regulates inflammatory factor release and neuronal apoptosis.