Suicide is an extreme consequence of the psychological burden associated with the coronavirus disease 2019 (COVID‐19) counter-measures. A quasi-Poisson regression was applied to monthly suicide mortality data obtained from the National Police Agency to estimate the gender-specific excess/exiguous suicide deaths during the COVID-19 pandemic in Japan up to September 2020. We found excess suicide deaths among women in July, August and September, but not among men. Our results indicate the importance of COVID-19 related suicide prevention, especially for women. Timely access to mental health care and financial and social support is urgently needed, as is optimal treatment for mental illness.