A school teacher’s job is considered one of the most stressful occupations globally. The coronavirus disease 2019 pandemic has posed further challenges for school teachers. This study aimed to examine the effects of the pandemic on primary school teachers’ stress responses in Japan. We analyzed the data from a nationwide survey of public-school teachers conducted between June 2019 and December 2021. The total numbers of participants were 65,968 in 2019, 72,248 in 2020, and 75,435 in 2021. Working hours and perceived main stressors as well as stress response scores were assessed. Contrary to expectations, the results showed that the stress response scores in primary school teachers did not increase in the first year of the pandemic. Rather, the stress response scores and the proportion of high-stress teachers significantly decreased from the pre-pandemic year (2019) to the first year of the pandemic (2020). However, the stress response scores showed a rising trend in the second year of the pandemic (2021). Participants’ working hours decreased from 2019 to 2021. The findings in relation to main stressors matched these trends. Continuous monitoring of teachers’ stress levels is recommended both during and after the pandemic.