Background Existing data on adverse effects of coronavirus disease 2019 (COVID-19) vaccines among university students are limited. This study aimed to investigate the characteristics of adverse effects that may arise from administering COVID-19 vaccines to university students in Thailand. Methods An online survey study was conducted among students from 12 Health Sciences faculties, and from 16 non-Health Sciences faculties of two universities from October 2021 to January 2022 to assess types and adverse effects of COVID-19 vaccines received by the students. Results There were 1,439 participating students; 522 (36%) were from Health Sciences faculties, and 917 (64%) were from 16 non-Health Sciences faculties. The types of the first-dose vaccine received were inactivated (49%), viral vector (46%), and mRNA (5%), while the types of the second-dose vaccine received were viral vector (53%), inactivated (40%) and mRNA (7%). The first-dose vaccines’ most common adverse effects of inactivated, viral vector, and mRNA vaccines were muscle pain (47%, 82%, and 58%, respectively). The second-dose vaccines’ most common adverse effects were cough (47%) for inactivated vaccines and muscle pain (49% for viral vector vaccines and 56% for mRNA vaccines). Viral vector vaccines were more likely to cause fever, muscle pain, diarrhoea, headache, and rashes than the others. The mRNA vaccines caused injection site pain more than inactivated vaccines. The majority of adverse effects occurred 24-48 hours after vaccination (68%), were more severe with the first dose compared with the second dose, and resolved spontaneously without any treatment at a hospital. Conclusions The adverse effects experienced by the students were various according to the types and number of doses of COVID-19 vaccines. The adverse effects were mostly non-severe and occurred less for the second dose compared with the first dose.