Cathepsin S plays an important role in the pathogenesis of several cardiovascular diseases; however, the relationship between serum cathepsin S and cerebral infarction (CI) is still unknown. This study aimed to investigate the relationship between acute phase serum cathepsin S level and cerebral infarction. A total of 202 stroke patients were enrolled into this study, and were divided into cerebral infarction (n = 140) group and non‐cerebral infarction group (non‐CI, n = 62). Fifty healthy individuals were recruited as the control group. Serum levels of cathepsin S and cystatin C were measured at days 1, 7, and 14 posthospitalization. Compared to the non‐CI group, the CI group had significantly higher rates of hypertension, dyslipidemia, and smoking (all P < 0.05). The CI group had significantly higher cathepsin S levels and cathepsin S to cystatin C ratio (CatS/CysC) at both days 1 and 7 posthospitalization (both P < 0.05). Multivariate logistic regression analysis demonstrated that cathepsin S level (day 7) and CatS/CysC (days 1 and 7) were the associated factors with CI (all P < 0.05). Receiver operating characteristic (ROC) curve analysis revealed that the Area Under Curve (AUC) value of CatS‐day7, CatS/CysC‐day1, and CatS/CysC‐day7 were 0.726 (95% CI: 0.652‐0.800, P < 0.001), 0.641 (95% CI: 0.559‐0.723, P = 0.001), and 0.721 (95% CI: 0.645‐0.797, P = 0.039), respectively. Cathepsin S and CatS/CysC were associated with acute CI, and may have the potential to be the diagnostic biomarkers for CI. Our findings help to better understand the role of serum cathepsin S level in CI.