Perceptions about illnesses may influence self-care and preventive health behaviours. Illness perceptions of the Zika virus (ZIKV) infection were investigated under the framework of the Self-Regulation Model of Illness. Illness perception differences between ZIKV and dengue fever were also examined. Lastly, associations between illness perceptions of ZIKV with mosquito prevention practices were studied. Samples were drawn from landline telephone numbers using computer-assisted telephone interviewing in Malaysia. A total of 567 respondents completed the survey between February 2015 and May 2016. The median and interquartile range (IQR) for the total six dimensions of illness perceptions score was higher for dengue (23.0 (IQR 17.0–28.0)) than ZIKV (20.0 (IRQ 11.0–28.0)), p < 0.001. Respondents who planned to have children (OR 1.670, 95% CI 1.035–2.694 vs. no intention to have children) and had friends or acquaintances who died of dengue (OR 2.372, 95% CI 1.300–4.327 vs. no friends who died of dengue) were more likely to have a higher total score for six illness perceptions for ZIKV compared to dengue. Multivariate analysis indicated that the best predictors for mosquito control practices after the ZIKV outbreak was declared a Public Health Emergency of International Concern, in descending order, were causes, control, timeline, and consequences dimensions of illness perception. Understanding the context in which a person perceives ZIKV may contribute to developing interventions that influence prevention behaviours.