Background-Thrombolysis has become an effective therapy for acute cerebral infarction (AIS) within 4.5 hours. Thrombolysis improves prognosis by increasing perfusion of the ischemic penumbra. Inflammation as one of the mechanisms of cerebral infarction, the role of thrombolysis is the topic of our exploration. Methods-From August 1, 2017 and September 1, 2019, 493 consecutive patients with AIS were prospectively enrolled in this cohort. 170 patients received thrombolytic therapy and 323 patients did not have thrombolysis. Clinical evaluation, laboratory data before and after thrombolysis and 3-month modified Rankin scale (mRS) scores were compared. Neutrophil-to-lymphocyte ratio (NLR), which represents inflammatory response, was divided into quartiles for comparison. Multivariate regression analysis was used to determine independent factors of 3-month prognosis. The receiver operating characteristic curve was used to evaluate the predictability of NLR for good prognosis that was defined as 3-month mRS scores < 3. Results-The NLR after thrombolysis was higher than that before thrombolysis (p < 0.001) and in non-thrombolytic patients (p < 0.001). NLR after thrombolysis is an independent predictor of 3-month functional outcome (odds ratio (OR) = 1.20, 95% confidence interval (CI), 1.01–1.42, p = 0.03). Also, a cutoff value of 4.51 for NLR was detected in predicting post-thrombolysis 3-month functional outcome with a sensitivity of 65.7% and a specificity of 73.1% (area under curve [AUC], 0.85; 95% CI, 0.77–0.92). We also found a significant difference (62% vs 88%, p < 0.001) in the proportion of good 3 months prognosis between the higher and lower group. Conclusions-This study showed that NLR increase after thrombolysis better predict post-thrombolytic unfavorable functional outcome in AIS patients. Clinical Trial Registration-URL: http://www.chictr.org.cn/index.aspx, Unique identifier: ChiCTR1800018315. URL: http://www.chictr.org.cn/index.aspx, Unique identifier: ChiCTR1800019615.