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Background: Qilong capsule (QLC) is a traditional Chinese medicine commonly used to treat ischemic stroke (IS). But the pharmacodynamic mechanism of QLC is not clear. Method: we used an existing zebrafish model to explore the protective mechanism of QLC on IS. We treated normally-developing zebrafish larvae with QLC and ponatinib 2 days post fertilization, and used the area of cerebral vascular thrombosis, red blood cell staining intensity, and brain cell apoptosis to quantitate QLC efficacy against IS. Real-time quantitative polymerase chain reaction (qPCR) was used to detect changes in the expression of genes involved in coagulation, inflammation, vascular endothelium, and apoptosis. Result: We found that QLC reduced the area affected by ponatinib-induced cerebral vascular embolism, erythrocyte staining intensity, and the number of apoptotic brain cells. qPCR showed that QLC inhibited the expression of genes related to coagulation, inflammation, and apoptosis. Conclusion: QLC had a significant protective efficacy in ponatinib-induced IS.