Objectives: This study examined the prevalence of anxiety, depression, and job burnout among frontline healthcare workers (HCWs) across six Southeast Asian countries (Indonesia, Malaysia, Philippines, Singapore, Thailand, Vietnam) during the COVID-19 pandemic in 2021. We also investigated the associated risk and protective factors. Methods: Frontline HCWs (N = 1381) from the participating countries participated between 4 January and 14 June 2021. The participants completed self-reported surveys on anxiety (GAD-7), depression (PHQ-8), and job burnout (PWLS). Multivariate logistic regressions were performed with anxiety, depression, and job burnout as outcomes and sociodemographic and job characteristics and HCW perceptions as predictors. Results: The average proportion of HCWs reporting moderate anxiety, moderately severe depression, and job burnout across all countries were 10%, 4%, and 20%, respectively. Working longer hours than usual (Odds ratio [OR] = 1.82; 3.51), perceived high job risk (1.98; 2.22), and inadequate personal protective equipment (1.89; 2.11) were associated with increased odds of anxiety and job burnout while working night shifts was associated with increased risk of depression (3.23). Perceived good teamwork was associated with lower odds of anxiety (0.46), depression (0.43), and job burnout (0.39). Conclusion: Job burnout remains a foremost issue among HCWs. Potential opportunities to improve HCW wellness are discussed.