This study addresses the crucial aspect of childhood COVID-19 vaccination and its impact on parental decisions concerning learning modalities during the pandemic. This study aimed to gauge parental hesitancy towards vaccinating their children and its influence on choosing between distance and face-to-face learning options. Following STROBE guidelines for cross-sectional studies, this study surveyed 1973 parents in the United Arab Emirates using Google Forms during the COVID-19 pandemic. The results revealed that while more than half of the parents (51.6%) were willing to vaccinate their children if the COVID-19 vaccine was accessible and affordable, a significant majority (91.2%) expressed concerns about the rapid vaccine development process, which was the primary reason for vaccine rejection. Interestingly, a sizable portion (55.3%) had experienced online learning in the previous academic term, and, of those, 59.6% believed it negatively influenced their children’s academic performance. Consequently, 66.4% expressed intent to shift their children back to face-to-face learning once feasible. Significantly, parents with medical backgrounds were more inclined (91.6%) to opt for face-to-face schooling compared to those without such backgrounds. Logistic regression analysis indicated associations between sociodemographic characteristics, educational level and background, and the decision to return children to face-to-face learning. Interestingly, when it comes to vaccine hesitancy, a noteworthy connection exists between the parents’ reluctance to vaccinate their children and their preference for distance learning. In fact, parents who responded negatively to vaccinating their children against COVID-19, if the vaccine was available, showed a clear preference for the distance learning modality (p-value < 0.0001). This study underscores the complex interplay of factors and community perspectives shaping parental acceptance of childhood COVID-19 vaccination. The development pace of vaccines significantly influences parents’ attitudes and beliefs about vaccination programs. Parents’ medical backgrounds exhibit a clear correlation with their perceptions of sending children back to school safely. This highlights the potential impact of parental medical knowledge on decision making, emphasizing the need to consider parents’ professional backgrounds when devising education- and vaccination-related policies.