Asian dust storms (ADS) have affected several Asian countries and have been a major concern due to adverse effects on public health. The occurrence of ADS differs in each country based on geographical features and distance from the storms' origin. Many studies have reported significant associations between ADS and morbidity. However, regarding the association between ADS and mortality, only a few studies have found statistically significant ADS effects in Korea, Taiwan and Japan. Accordingly, this study aimed to examine the effects of ADS on daily mortality in three Asian cities (Seoul, South Korea; Taipei, Taiwan; and Kitakyushu, Japan) and to explore the differences in the extent of effects in each city. We performed time-series analyses using a generalized additive model (GAM) with Quasi-Poisson regressions. Deaths due to accidents or external causes were excluded. We used a dummy variable as an indicator of ADS and considered lag effects of ADS. Stratified analyses by disease and age and sensitivity analyses controlling for NO2, SO2, and PM10 were also conducted respectively. Additionally, influenza epidemics were adjusted for considering seasonal patterns, and a meta-analysis was performed. We reported results as excess mortality by percentage due to Asian dust storms. We found significant excess mortality in Seoul and Kitakyushu as follows. In Seoul, ADS showed adverse effects on mortality under 65 years old (lag 2: 4.44%, lag 3: 5%, lag 4: 4.39%). In Kitakyushu, ADS had adverse effects on respiratory mortality (lag 2: 18.82%). Contradictory to results in Seoul and Kitakyushu, ADS seemed to have a protective effect in Taipei: total non-accidental mortality (lag 0: −2.77%, lag 1: −3.24%), mortality over 65 years old (lag 0: −3.35%, lag 1: −3.29%) and respiratory mortality (lag 0: −10.62%, lag 1: −9.67%). Sensitivity analyses showed similar findings as the main results. Our findings suggest that ADS may affect mortality in several Asian cities, and that a dust storm warning system could help protect people from dust storms.