The COVID-19 pandemic in Estonia was a part of the ongoing worldwide pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

The virus was confirmed to have spread to Estonia when the first case was confirmed in Tallinn on 27 February 2020.^[3] By 11 March, 15 people in Estonia had been diagnosed with the virus. All of them had been infected outside the country, mostly in Northern Italy.^[4][5] On 12 March, the first cases of locally transmitted infections emerged,^[6] and on 13 March, the Estonian government declared a state of emergency until 1 May 2020. As a result, all schools and universities were closed, and all public gatherings were banned, including sports and cultural events.^[7] Later the state of emergency was extended until 17 May.^[8]

Saare County was the hardest hit county in Estonia by the COVID-19 during spring. It has only 2.5% of the population of Estonia, but in March, it had over half of all hospitalized patients.^[9] Coronavirus was allegedly brought there by the Italian volleyball club Power Volley Milano, which participated in the 2019–20 CEV Challenge Cup matches held on Saaremaa island on 4 and 5 March. The virus may have spread rapidly in the community through a champagne festival held later on. Health officials estimate that half of the island's population have contracted the virus so far.^[10][11][12] In autumn during the second wave, Ida-Viru County and Harju County were hit hardest.^{[citation needed]}

At the beginning of the pandemic, most of the cases came in from Austria and Italy,^[13] but in the second part of the year 2020, Russia, Ukraine, and Finland took the lead.^[14]

In the first months of 2021 situation grow worse and by mid-March Estonia had the most new cases per capita in the world.^[15] Starting from March 11 stronger measures were taken to suppress the spread of the virus.

As of 21 January 2023, 2,192,989 COVID-19 vaccine doses had been administered in Estonia.^[16]

On 12 January 2020, the World Health Organization (WHO) confirmed that a novel coronavirus was the cause of a respiratory illness in a cluster of people in Wuhan City, Hubei Province, China, which was reported to the WHO on 31 December 2019.^[17][18]

The case fatality ratio for COVID-19 has been much lower than SARS of 2003,^[19][20] but the transmission has been significantly greater, with a significant total death toll.^[19][21]