Background and purpose Since the outbreak of the coronavirus pandemic in 2019 (COVID-19), healthcare systems around the world have been hit to varying degrees. As a neurologist team, for patients with acute ischemic stroke (AIS), we compared the situations of intravenous thrombolysis (IVT) treatment from 2019 to 2020 to investigate the influence of COVID-19 pandemic on the attendance and prognosis of the IVT patients. Methods We collected the messages of objects who had received IVT (Bridging surgery was ruled out) during 2019–2020. We analyzed differences in age, gender, time from onset to start IVT, door to needle time (DNT), pretreatment NIHSS score, postoperative NIHSS score, and so on. Statistical tests were also performed to respectively compare the discharged modified Rankin score (mRS) and discharged NIHSS score between two years. Results Since the onset of COVID-19 restrictions in Wenzhou, we observed a significant reduction of 24.7% ( p = 0.023) from 267(2019) to 201(2020) of received IVT on hospital admission. We compared the DNT between two years and it reflected that the DNT (min) in 2020 was obviously longer than in 2019 (51.60 ± 23.80 vs 46.80 ± 21.90, p = 0.026). We also compared the discharged mRS, which reflected much more IVT patients in 2020 during the COVID-19 pandemic had a poor short-term functional prognosis (38.2% vs 29.2%, p = 0.043). Conclusions The COVID-19 pandemic caused the decrease of admissions and prolonged the time of the green channel for stroke, which led to the worse short-term prognosis of AIS patients during the pandemic. It’s necessary to ensure an effective green channel and provide adequate medical resources during the pandemic period to reduce the damage caused by COVID-19.