Objective Although healthcare workers (HCWs) experienced significant stress during the 2015 outbreak of Middle East Respiratory Syndrome (MERS), the factors associated with this stress remain unknown. Thus, the present study assessed burnout among HCWs during the MERS outbreak to identify the influential factors involved in this process. Methods This study was a retrospective chart review of the psychological tests and questionnaires completed by 171 hospital employees from two general hospitals that treated MERS patients. The tests included the Oldenburg Burnout Inventory, Positive Resources Test, the questionnaires assessed exposure to the MERS outbreak event and perceptions about MERS. Results Of the 171 HCWs, 112 (65.5%) experienced disengagement and 136 (79.5%) suffered from exhaustion. Disengagement was associated with lower levels of purpose and hope, a higher perception of job risk, and exposure to the media. Exhaustion was associated with lower levels of purpose and hope, a higher perception of little control of the infection, a higher perception of job risk, prior experience related to infections, and being female. Conclusion Our results revealed the risk and protective factors associated with burnout among HCWs during an outbreak of MERS. These findings should be considered when determining interventional strategies aimed at ameliorating burnout among HCWs.