Vaccine acceptance in the general public is essential in controlling the coronavirus disease 2019 (COVID-19) pandemic. The study aimed to assess the COVID-19 vaccine hesitancy in the adult population of Mongolia, and determine the associated factors. A total of 2875 individuals from urban and rural areas were recruited, and completed an online survey. Older age, urban residence, previous vaccination, high education, good knowledge of side effects, and a personal view of the importance of vaccines were associated with vaccine acceptability, whereas gender and religion were not. Receiving COVID-19 vaccine information from official government pages was related to a higher acceptance rate. Reliance on social media as a source of COVID-19 vaccine information was associated with high level of vaccine hesitancy. The side effects and the type of the COVID-19 vaccine were a major reason for hesitation. Countering false information regarding COVID-19 vaccines on social media, and promoting vaccine importance on general news websites is necessary. Moreover, providing clear and direct educational materials through official communication channels on the safety and efficacy of COVID-19 vaccines alongside information on COVID-19 symptoms, vaccine side effects, and location of vaccine administration centers among the younger populations, rural residents, and those with lower education is needed.