The following is a timeline of the COVID-19 pandemic in Japan.

Background The COVID-19 pandemic in Japan can be divided into five waves based on the genome sequence of the country's COVID-19 virus. The National Institute of Infectious Diseases (Japan) (NIID) has determined from its genetic research that the COVID-19 variant of the first wave is derived from the Wuhan type that is prevalent in patients from China and East Asia. After entering Japan in January through travellers and returnees from China, the virus resulted in numerous infection clusters across the country before moving towards its disappearance in March. Japanese medical surveillance confirmed its first case of the virus on 16 January in a resident of Kanagawa Prefecture who had returned from Wuhan.

The first wave was followed by a second one that originated from a COVID-19 variant of the European type that is traced back to early patients from France, Italy, Sweden, and the United Kingdom. Japanese medical surveillance detected the second wave on 26 March when the government's expert panel concluded the likelihood of a new outbreak caused by travellers and returnees from Europe and the United States between 11 and 23 March. The NIID has established that the majority of viruses spreading in Japan since March is the European type. This has led it to conclude that the data "strongly suggests" that the Japanese government has succeeded in containing the Wuhan variant and that it is the European variant that is spreading across the country.Virus strain in Japan possibly spread via Europe, U.S. since March. The Japan News (29 April 2020).Retrieved 4 May 2020.

Initial outbreak (January–March 2020)

January 2020 On 16 January, Japan confirmed its first case of COVID-19 when a man in Kanagawa Prefecture who had previously travelled to Wuhan tested positive.

On 24 January, Tokyo Metropolis confirmed its first case of COVID-19. The Japanese government announced that it would provide repatriation services for all Japanese citizens in Hubei Province on that same day. Officials negotiated with Chinese authorities to dispatch five chartered flights to Wuhan from 29 January to 17 February.

On 27 January, Prime Minister Shinzo Abe labelled COVID-19 as a "designated infectious disease" under the and a "quarantinable infectious disease" under the Quarantine Act. On 30 January, Abe announced the establishment of a national task force to oversee the government's countermeasures against the novel coronavirus.

On 28 January, Nara Prefecture and Hokkaido Prefecture confirmed their first cases of COVID-19. On 29 January, Osaka Prefecture reported its first case on 29 January, followed by Mie Prefecture and Kyoto Prefecture on 30 January, and Chiba Prefecture on 31 January.

February 2020

On 1 February, a passenger of the Diamond Princess cruise ship who had visited Hong Kong earlier tested positive. Although the ship had already completed quarantine at Naha en route to Yokohama, the government ordered the ship to re-quarantine in Yokohama.

On 3 February, the government announced entry restrictions for foreign citizens who had travelled in Hubei Province or had a Chinese passport issued from there.

On 12 February, the government announced entry restrictions for all foreign citizens who had travelled in Zhejiang Province or had a Chinese passport issued from there.

On 13 February, Wakayama Prefecture confirmed its first case of COVID-19. Japan announced its first COVID-19 fatality, a woman in her 80s from Kanagawa Prefecture. It was the third COVID-19 death outside mainland China.

On 14 February, Okinawa Prefecture confirmed its first case, followed by Aichi Prefecture on the 15th. On 20 February, Saitama and Fukuoka Prefectures confirmed their first cases of COVID-19. On 21 February, Ishikawa Prefecture and Kumamoto Prefecture reported their first cases, followed by Tochigi Prefecture on 22 February.

On 23 February, the US State Department raised its travel alert for Japan to level 2 on the four-level advisory scale due to the "sustained community spread" of COVID-19 within the country.

On 25 February, Nagano and Tokushima Prefectures reported their first cases, followed by Gifu Prefecture on 26 February.

On 27 February, Prime Minister Abe requested the closure of all elementary, junior high, and high schools from 2 March to the end of spring vacations in early April.

On 28 February, Hokkaido Prefecture declared a state of emergency and asked residents to refrain from going outside. Shizuoka Prefecture confirmed its first case of COVID-19 on that same day. On 29 February, Miyagi Prefecture, Kochi Prefecture, and Niigata Prefecture confirmed their first cases of COVID-19.

March 2020 On 1 March, Hyogo Prefecture confirmed its first case of COVID-19. Ehime Prefecture reported its first case on 2 March, followed by Oita Prefecture on 3 March; Yamaguchi Prefecture and Miyazaki Prefecture on 4 March; Shiga Prefecture on 5 March; Akita Prefecture and Yamanashi Prefecture on 6 March; and Hiroshima Prefecture and Gunma Prefecture on 7 March.

On 2 March, schools were closed in almost all prefectures. Expanded rules for governmental paid leave for workers were announced.

On 5 March, Japan announced quarantine restrictions for all visitors arriving from China and South Korea. On 6 March, the South Korean government protested the restrictions by suspending visas for all Japanese citizens travelling to South Korea.

On 10 March, Japan officially classed the coronavirus outbreak as a national emergency. The government announced a 1 trillion yen ($9.6 billion) emergency package for businesses, including zero-interest loans for small and midsize companies and subsidies for freelance workers. Prime Minister Abe asked that large events be cancelled or postponed so that measures for containing the virus could be evaluated.

On 12 March, Japan reported 4 deaths from COVID-19.

On 13 March, Saga Prefecture confirmed its first case of COVID-19. Nagasaki Prefecture reported its first case on 14 March, followed by Ibaraki Prefecture and Kagawa Prefecture on 17 March, and Fukui Prefecture on 18 March.

On 16 March, the Japanese government announced it would expand entry restrictions to all foreign citizens of three areas in Spain, four areas in Italy, the Ticino region of Switzerland, and all of Iceland.

On 19 March, the governors of Osaka and Hyogo prefectures asked residents to avoid nonessential travel between the two neighbouring prefectures over the three-day weekend starting on 20 March. The three-week state of emergency in Hokkaido was lifted on that same day.

On 22 March, Okayama Prefecture confirmed its first case of COVID-19 and asked its residents to refrain from visiting the neighboring prefectures of Hyogo and Osaka. Aomori Prefecture reported its first case on 23 March, followed by Gifu Prefecture on 26 March.

On 23 March, Tokyo governor Yuriko Koike warned residents that a lockdown might be imposed if infections increased in Tokyo.

On 24 March, the International Olympic Committee (IOC) and Tokyo Organising Committee of the Olympic and Paralympic Games announced a one-year postponement of the 2020 Summer Olympics.

On 25 March, Ministry of Health, Labour and Welfare (MHLW) officials announced 71 people tested positive, including 41 cases in Tokyo. Governor Koike held an emergency press conference in the late afternoon to reaffirm the seriousness of the situation and asked people remain inside voluntarily for the next two weeks. Panic buying began following the announcement.

On 26 March, several governors of the Greater Tokyo Area, including Chiba, Kanagawa, Saitama, and Yamanashi, urged residents to follow stay-at-home requests to prevent a surge in infections. In Tokyo, residents were asked to work from home and refrain from going out at night and on the weekend.

On 27 March, MHLW officials announced 112 people had tested positive in a single day, including three Hanshin Tigers professional baseball players.

On 28 March, Prime Minister Abe held a press briefing about economic measures being prepared by the Japanese government amid concerns of infections increasing. Abe's wife was accused of attending a hanami party in defiance of COVID restrictions, which Abe denied.

On 28 March, 63 people tested positive in Tokyo.

On 29 March, MHLW officials announced 194 people had tested positive, including 58 people at a facility for the disabled in Tōnoshō, Chiba Prefecture. That day, 68 people tested positive in Tokyo, for a total of 430 confirmed cases of COVID-19, the largest among Japan's 47 prefectures.

On 30 March, tarento and comedian Ken Shimura died at the age of 70 from complications of a COVID-19 infection. It was the first major COVID death in Japan's entertainment industry.

On 30 March, Fukuoka City confirmed that an infant under one year old was infected; the infection of children that young was a rarity. On 30 March, Toyama Prefecture announced its first case, and a Kyoto government official announced several cases at Kyoto Sangyo University, including two students who had recently returned from Europe.

On 31 March, Tokyo reported 7 deaths and 78 new infections, for a total of 521 cases. 10 of the new cases were suspected to be tied to Eiju General Hospital in Taito Ward. Calls were made for the prime minister to declare a state of emergency, but both Prime Minister Abe and Chief Cabinet Secretary Suga denied that it was necessary.

April 2020–June 2020

April 2020

On 1 April, the government established a team to determine Japan's response to the coronavirus outbreak as well as other national challenges.

On 3 April, Japan expanded its entry ban to cover 73 countries and regions, barring entrance to the country to all foreigners, including those with Japanese residency or permanent residency, who had been in those parts of the world within 14 days of their arrival in Japan. The same day, Immigration Services Agency of Japan said it would extend the deadline for foreigners to renew their visas, so that their service centers would not be overwhelmed by demand.

On 4 April, 118 new cases were announced in Tokyo. Public pressure increased for Prime Minister Abe to declare a state of emergency, which he had been reluctant to do.

On 6 April, 83 new coronavirus cases were reported in Tokyo. The city's government planned to transfer patients with mild symptoms from hospitals to quarantine facilities to free up beds for patients with serious symptoms.

On 7 April, Abe proclaimed a state of emergency from 8 April to 6 May for Tokyo and the prefectures of Kanagawa, Saitama, Chiba, Osaka, Hyogo and Fukuoka, but said there would be no lockdown measures. It was the first time a state of emergency had been declared in Japan. According to the Prime Minister, the pandemic had created the worst economic crisis in Japan since World War II.

On 8 April, Tokyo confirmed 144 new coronavirus cases. Infection routes could not be determined for over 60% of them.

On 10 April, Nippon Professional Baseball and the J-League cancelled all games in April.

On 11 April, 197 new coronavirus cases were confirmed in Tokyo, for a total of over 1,900 cases in the city.

On 12 April, Narita International Airport closed one of its two runways due to an 85 percent reduction in traffic caused by the virus.

On April 13, a second wave of infections hit Hokkaido, prompting the prefectural government to declare a second state of emergency that closed schools and that asked residents to avoid non-essential trips.

On 16 April, the government expanded the state of emergency to include all 47 prefectures in Japan and announced a plan to give 100,000 yen to every registered resident of Japan as a stimulus measure.

On 19 April, the first COVID death in the Chūgoku region was reported, in Hiroshima Prefecture.