Introduction: The aim of our study was to determine whether the severity of the COVID-19 pandemic affected the quality of acute care of stroke. Methods: Data from the stroke register at the National Health Information Centre were analysed. Clinical data from two time periods (the first wave: March–April 2020; the second wave: October–November 2020) were compared using an independent sample t-test and the Wilcoxon-Mann-Whitney two sample rank-sum test. Results: The total number of patients admitted with stroke during the second wave of COVID-19 was 1848, versus 1698 in the first wave. The proportion of patients treated by IVT was similar in both waves (275 (20.7%) vs 333 (22.1%), p = 1, difference in location: −0,0003, 95% CI: −5.0 to 5.95). We found no difference in time from the onset of symptoms to treatment (median = 130 min in both waves, p = 0.52, difference in location: 3.99, 95% CI: −6.0 to 14.0), nor in the door-to-needle time (median = 29 vs 30 min, p = 0.08, difference in location: −2.99, 95% CI: −5.0 to 0.008) between the first and the second waves of the pandemic. We found no difference in NIHSS (median = 3 vs 4, p = 0.51, difference in location: 0.00007, 95% CI: −0.9 to 0.000006) and mRS (median = 3 in both waves, p = 0.60, difference in location: −0.00004, 95% CI: −0.00004 to 0.00003) at discharge from hospital between the two periods. Conclusion: The severity of the COVID-19 outbreak did not affect the quality of acute stroke care in Slovakia.