In Japan, suicide mortalities consistently decreased before the COVID-19 pandemic (from 2009 to 2019) but, conversely, increased after the pandemic outbreak from 2020 to 2022. To provide up-to-date suicide statistics in Japan, this study determined the temporal fluctuations of standardized suicide mortalities (SMRs), disaggregated by sex and age, by joinpoint regression analysis using the government suicide database, named the “Basic Data on Suicide in Region”. From January 2009 to December 2023, three temporal fluctuation patterns of SMRs pertaining to working age and older adults were detected, such as attenuations of decreasing trends before the COVID-19 pandemic (from around the mid-2010s), a sharply increasing trend that coincided with the pandemic outbreak, and gradually decreased during the pandemic, but no changes at the end of the COVID-19 pandemic. In particular, the SMRs of working-age females sharply increased concurrently with the pandemic outbreak, whereas those of males did not change. However, before the pandemic, decreasing trends of the SMRs of working-age males diminished in the mid-2010s, but those of females consistently decreased. The SMRs of working-age males indicated non-significant but sharply increasing trends in early 2022, a trend that was not observed for females. In contrast to working-age adults, the SMRs of adolescents already began to increase in the mid-2010s and also indicated consistently increasing trends between the periods during and after the pandemic. These results suggest, contrary to our expectations, that the impacts of both the outbreak and end of the COVID-19 pandemic were limited regarding the increase in SMRs from 2020. Therefore, when revising suicide prevention programs in the post-COVID-19 era, it should be noted that focusing on pandemic-associated factors alone is not sufficient.