The current study aimed to explore Palestinian university students’ perceptions and concerns about COVID-19 vaccination hesitancy. Our sample comprised 50 university students selected using snowball sampling techniques from Palestinian universities in the West Bank, Palestine. Thematic content analysis was conducted to identify the main themes of semi-structured interviews with students. The results of the thematic content analysis yielded four main themes: Students’ perceptions and concerns on COVID-19 vaccinations, perceived risks of vaccination, experiences related to vaccination, and causes of vaccination hesitancy. Participants expressed concerns and doubts about the vaccine’s safety, showing high hesitancy and scepticism; they also reported different causes for COVID-19 vaccination hesitancy in the Palestinian context, such as the lack of confidence in vaccines, false beliefs about vaccines, and peculiar political instability and conflict of the Palestinian territories enduring a military occupation undermining the health system’s capacity to respond to the COVID-19 outbreak appropriately. Health authorities and policymakers are urgently called to invest in and potentiate awareness campaigns to change the diffuse people’s stereotypes related to the COVID-19 vaccine in the Palestinian territories.