The current academic landscape has overwhelmed faculties and with demands to adopt tech-savvy teaching modes and accelerate scholarly works, administrative duties, and outreach programs. Such demands have deteriorated the health-related quality of life (HRQoL) among university employees. This study aimed to determine the factors associated with HRQoL among university employees in a Malaysian public university. This cross-sectional study was conducted among 397 employees from the Universiti Kebangsaan Malaysia (UKM) between April and June 2019. A self-administered questionnaire that consisted of socio-demographic items, risky health behaviors, health-related information, and validated scales for measuring employees' physical inactivity, psychological states, and HRQoL was utilized. Descriptive and inferential statistics were calculated using SPSS version 23.0. Hierarchical multiple linear regression models were yielded to determine the factors associated with different domains of HRQoL. Mediation analysis was conducted using PROCESS MACRO (Model 4). Statistical significance was set to p < 0.05. Physical HRQoL scored the highest, while environmental HRQoL had the lowest score among the employees. Physical HRQoL was influenced by age, service duration, comorbid conditions, BMI, chronic diseases, and anxiety. Factors associated with psychological HRQoL were age, service duration, depression, and stress. Age, service duration, and chronic diseases affected employees' social relationship HRQoL, while environmental HRQoL was associated with age, occupation type, chronic diseases, and depression. Socio-demographics, risky health behaviors, health profiles, and psychological attributes were significantly associated with employees' HRQoL. Age was the only positively correlated factor across all HRQoL domains, while other factors deteriorated employees' HRQoL.