Objectives: Health-related quality of life (HRQoL) is an essential dimension of overall human quality of life, in which disparities have been hypothesised between women and men, as well as between citizens and non-citizens of a country in past literatures. This study is to evaluate and compare the HRQoL of citizens and non-citizens living in greater Kuala Lumpur and Johor Bahru, as well as comparing HRQoL between genders. Materials and Methods: The SF-8 questionnaire was used to collect information from 1,708 respondents (1,032 Malaysian citizens and 676 non-citizens), via face-to-face interview between October and December 2015. Results: Overall, respondents reported moderate HRQoL. Non-citizens reported better HRQoL than the Malaysian citizens, while men reported better HRQoL compared to women (for both citizens and non-citizens). Conclusions: The HRQoL of both citizens and noncitizens’ in Malaysia could be improved. Measures should be taken to remove the disparity in HRQoL between men and women, aiming to achieve equal health status for both genders.