The novel coronavirus disease 2019 (COVID-19) pandemic has spread rapidly worldwide. To prevent the spread of COVID-19, mRNA-based vaccines made by Pfizer/BioNTech (BNT162b1) and Moderna (mRNA-1273) have been widely used worldwide, including in Japan. Various adverse events after COVID-19 mRNA vaccinations have been reported, with differences observed among individuals. However, the analysis on the genetic background for susceptibility to side effects has been limited. In the present work, we performed genome-wide association studies (GWAS) for self-reported adverse events of COVID-19 mRNA vaccination in 4,545 Japanese individuals and identified 14 associated loci. Among these, 6p21 was associated with 37.5°C or higher fever, 38 °C or higher fever, and muscle pain. Our results may enable one to prepare for and manage side effects by knowing their susceptibility to the occurrence of adverse events. Furthermore, we obtained valuable data that can lead to the understanding of the mechanism of action of COVID-19 mRNA vaccines.