Background and Objectives: COVID-19 remains a major development challenge in many developing countries. This study analysed the effect of mental health disorder and indicators of COVID-19 preventive practices on vaccination intentions among refugees in Kenya. Materials and Methods: The data were the fourth and fifth waves of the High Frequency Phone Surveys on the impacts of COVID-19 that were collected by the Kenyan National Bureau of Statistics (KNBS) between May 2020 and June 2021. The data were collected from Kakuma, Kalobeyei, Dadaab and Shona camps using the stratified random sampling method. The data were analysed with random effects instrumental variable Probit regression model. Results: The results showed that 69.32% and 93.16% of the refugees were willing to be vaccinated during the 4th and 5th waves, respectively. The fear of dying was reported by 85.89% and 74.19% during the 4th and 5th waves, respectively. COVID-19 contact prevention and immune boosting indicators were differently influenced by some demographic and anxiety index variables, while being endogenous influenced vaccine hesitancy along with urban residence, age, knowing infected persons, days of depression, days of anxiety, days of physical reactions, members losing job, searching for jobs, accepting job offers and being employed. Conclusions: It was concluded that efforts to promote COVID-19 vaccination should address mental health disorder and compliance with existing COVID-19 contact and immune boosting behaviour with a focus on urban residents and youths.