Currently the world is threatened by a global COVID-19 pandemic and it has induced crisis creating a lot of disruptions in the healthcare system, social life and economy. In this article we present the analysis of COVID-19 situation in Lithuania and it's municipalities taking into consideration the effect of non-pharmaceutical interventions on the reproduction number. We have analysed the period from 20/03/2020 to 20/06/2021 covering two quarantines applied in Lithuania. We calculated the reproduction number using the incidence data provided by State Data Governance Information System, while the information for applied non-pharmaceutical interventions was extracted from Oxford COVID-19 Government Response Tracker and the COVID-19 website of Government of the Republic of Lithuania. The positive effect of applied non-pharmaceutical interventions on reproduction number was observed when internal movement ban was applied in 16/12/2020 during the second quarantine in Lithuania.