School teachers have faced many challenges due to the coronavirus disease-2019 (COVID-19) pandemic and public health-related containment measures. Recent studies have demonstrated high levels of stress and mental health issues among school teachers. To better understand teacher well-being and inform practices to support them in the face of the ongoing pandemic, we aimed to assess perceived stress, well-being and associated factors among school teachers in Hong Kong, China. For this cross-sectional study, we employed a self-reported questionnaire to assess teacher well-being as an indicator of mental health. Drawing on quantitative data obtained from 336 teachers in Hong Kong from April 2021 to February 2022, we assessed workloads, work-related sense of coherence, perceived stress, secondary burnout symptoms (i.e. intensification of work and exhaustion related to work situation), self-endangering work behaviours and satisfaction with work. Bivariate and multivariate analyses were performed to examine the associations between well-being, demographic and work characteristics. A high percentage (87.6%) of teachers had high levels of perceived stress, which was positively associated with extensification of work (r = 0.571, p < 0.01), intensification of work (r = 0.640, p < 0.01) and exhaustion related to work situation (r = 0.554, p < 0.01). A multilinear regression model adjusted for age and gender was computed to detect predictors of teachers’ well-being index values (F(12, 296) = 41.405, p < 0.001, R² = 0.627). A higher WHO-5 score was associated with (1) higher teaching hours (B = 0.235, 95% CI = 0.093, 0.413, p = 0.002); (2) higher work-related sense of coherence (B = 2.490, 95% CI = 0.209, 4.770, p = 0.032); (3) higher work satisfaction (B = 5.410, 95% CI = 2.979, 7.841, p < 0.001); (4) lower level of exhaustion related to work situations (B = −9.677, 95% CI = −12.279, −7.075, p < 0.001); and (5) lower level of psychosomatic complaints (B = −4.167, 95% CI = −6.739, −7.075, p = 0.002). These findings highlight the critical need to allocate more attention and resources to improve the mental health of school teachers in Hong Kong. The findings can also inform the development of psychological and organisational interventions and support mechanisms for teachers during the prolonged COVID-19 pandemic and in preparation for future stressful scenarios. Safeguarding the well-being and mental health of teachers is important for improving the quality of teaching and learning environments and the mental health of school students.