The COVID-19 pandemic generated an overload of the health system and mental, emotional, and physical exhaustion of workers. Previous studies have reported elevated levels of burnout syndrome in healthcare workers. The objective of the study was to estimate the prevalence and associated factors of burnout syndrome in healthcare workers. A cross-sectional study was conducted through the administration of an email survey during the second wave of COVID-19 cases. Burnout was evaluated using the Maslach Burnout Inventory questionnaire. The prevalence of burnout was estimated and the associated factors were analyzed using multivariate logistic regression analysis. The 84% of the participants completed the survey (N = 133), 106 were physicians (80%), 11 administrators (8%), 9 respiratory physiologists (7%), and 7 nurses (5%). 62% were women. The prevalence of burnout was 38% (95% CI 30-47%) and it was different according to the occupation (p = < 0.001). Physicians and respiratory kinesiologists presented the highest values with a prevalence of 40% and 89% respectively. In the multivariate analysis, the variables that were independently associated with the burnout syndrome were: being a physician (OR = 8.9; 95% CI: 1.1-71; p: 0.041) and being a respiratory kinesiologist (OR = 137.5; 95% CI: 2-262; p 0.001). The prevalence of burnout syndrome in healthcare workers during the COVID-19 pandemic was high. Mainly in respiratory kinesiologists and physicians.