The transition from online to on-site education was difficult due to a lack of standardized school guidance for school reopening. Even though schools have reopened, uncertainty about the COVID-19 situation and the capacity of the school to maintain safe school operations to mitigate risks may increase hesitancy among students and parents to participate in on-site studying. Rapid-response surveys of students and parents can provide information to stakeholders on how learning and well-being can best be supported during the educational transition in each context. The aim of this study was to explore the hesitancy of high-school students and the factors that influenced their hesitancy to return to school on site. An online cross-sectional survey was distributed to high-school students in an urban district of Chiang Mai, Thailand, during the fourth wave of the pandemic from 17 November to 13 December 2021. A multivariable logistic regression was performed to explore factors related to the students’ hesitancy to attend on-site education. With a response rate of 10.2% of the targeted study population, the 1266 participants revealed that 15.9% of them had very-high- and extremely high-level hesitancy to study on site, which was associated with less negative moods while studying online (aOR, 1.69; p, 0.016) and a greater fear of infection after returning to school (aOR, 2.95; p, 0.001). Increased readiness to return to school on site (aOR, 0.28; p, 0.001) and discussing COVID-19 prevention with family or friends (aOR, 0.71; p, 0.016) were also associated with a lower hesitancy of students. Only 5.6% of the students reported being hesitant to receive the COVID-19 vaccination. However, no significant associations were found between schooling hesitancy and their willingness to get vaccinated, nor the frequency of students’ outside activities. High-school students who experience negative moods during online studying should be monitored and receive additional support if the reopening is postponed. More opportunities to discuss COVID-19 prevention with family or friends, as well as a higher level of readiness, may increase the willingness to return to school on site. Local authorities and schools need to strengthen communication and coordination mechanisms to reduce parents’ and students’ schooling hesitancy by providing explicit information about the COVID-19 situation and risk-mitigation measures, along with normalizing messages about fear and anxiety.