This study aimed to examine and compare the extent of burnout among health science faculty at a higher education institution and their self-reported perception of well-being during the COVID-19 pandemic. The design of the study was cross-sectional, descriptive survey research. An electronic questionnaire was developed to measure the constructs of burnout and well-being. Validated instruments used in the survey included the Oldenburg Burnout Inventory (OLBI) and the World Health Organization-5 Well-being Index. The Qualtrics ® platform was used to distribute the survey to all full-time faculty within the College of Health Sciences. 45 respondents from nursing, community and environmental health, kinesiology, social work, respiratory care, allied health sciences, and radiologic sciences completed the survey. Significant differences were observed in the extent of burnout and perception of well-being between faculty members who had clinical teaching responsibilities within their faculty role compared to those who did not, p = 0.005, Partial Eta Squared = 0.318. Faculty with a 9-month contract appointment had significantly lower OLBI-Disengagement scores (p = 0.024) and OLBI-Full Burnout scores (p = 0.047) compared with those with another contract length. There was a significantly negative relationship between the extent of burnout and perception of well-being. In this sample of health science faculty, burnout, as characterized by increased exhaustion and disengagement, was moderately prevalent and associated with poorer well-being.