Background During the COVID-19 vaccination, the access to vaccines has been unequal among countries and individuals, for example low-income countries displayed significant low levels of vaccination. Furthermore, most refugees are living in developing low-income countries which struggling to access the essential health-care services including vaccination. Thus, the objective of this study was to assess the experiences and perceptions of COVID-19 infection and vaccination among Palestine refugees in Jerash camp compared to resident Jordanian citizens. Methods A face-to-face interview-based comparative cross-sectional study was carried out among Palestine refugees in Jerash camp located in northern Jordan and Jordanian citizens from different cities in Jordan from October, 2021 to March, 2022. A Chi-square test was used to determine the differences in the experiences and perceptions of COVID-19 infection and vaccination between Palestinian refugees and resident Jordanian citizens. Logistic regression analysis was performed to predict factors associated with the beliefs, barriers and hesitancy towards COVID-19 vaccines. Results The total number of participants was 992, with 501 (50.5%) Palestinian refugees and 491 (49.5%) Jordanian citizens. Most participants (64.1%) who have never been tested for COVID-19 were from the refugees (P < 0.001), whereas about 80.3% of the participants tested for COVID-19 at private healthcare institutions were citizens (P < 0.001). While 70.0% of the participants who tested positive for COVID-19 (n = 303) were from the refugees (P < 0.001). Compared to the citizens, the refugees had significantly lower levels of beliefs about the safety (P = 0.008) and efficiency (P < 0.001) of COVID-19 vaccines. They also had lower rates of vaccine hesitancy (P = 0.002) and vaccine uptake (P < 0.001), and a higher rate of facing difficulties during registration for COVID-19 vaccination (P < 0.001). Furthermore, refugees have more negative attitudes toward the importance and implementation of COVID-19 precautionary activities, including wearing face masks, practicing social distancing and following proper prevention hygiene compared to citizens (P < 0.001). The regression analysis showed that gender (P < 0.001), age (P < 0.001) and level of education (P = 0.001) were significantly associated with COVID-19 vaccine hesitancy. Also, being a refugee (P < 0.001) and being a male (P = 0.012) were significantly associated with facing more difficulties upon the registration to receive a COVID-19 vaccine. Conclusions This study showed that, compared to citizens, refugees had lower attitudes and practices toward COVID-19 infection and vaccination. They also had and a lower rate of COVID-19 vaccine hesitancy and uptake with limited access to vaccines. Government sectors and non-government organizations should implement policies and regulations to raise the awareness of refugees towards COVID-19 infection, testing, preventive measures, and the safety and efficacy of vaccines.