Prior research has indicated that pollen might be linked to suicide mortality although the few studies that have been undertaken to date have produced conflicting findings and been limited to Western settings. This study examined the association between the level of airborne pollen and suicide mortality in Tokyo, Japan in the period from 2001 to 2011. The daily number of suicide deaths was obtained from the Japanese Ministry of Health, Labour and Welfare, with pollen data being obtained from the Tokyo Metropolitan Institute of Public Health. A time-stratified case-crossover study was performed to examine the association between different levels of pollen concentration and suicide mortality. During the study period there were 5185 male and 2332 female suicides in the pollen season (February to April). For men there was no association between airborne pollen and suicide mortality. For women, compared to when there was no airborne pollen, the same-day (lag 0) pollen level of 30 to <100 grains per cm2 was associated with an approximately 50% increase in the odds for suicide (e.g. 30 to <50 grains per cm2: odds ratio 1.574, 95% confidence interval 1.076–2.303, p=0.020). The estimates remained fairly stable after adjusting for air pollutants and after varying the cut-points that defined the pollen levels. Our results indicate that pollen is associated with female suicide mortality in Tokyo.