Background Malaysia has been experiencing an escalation in dengue cases since the past 5 years. As the dengue vaccine pipeline continues to develop steadily with strong public interests, this study had been sought to elicit the acceptance and the willingness to pay (WTP) for hypothetical dengue vaccine in Malaysia. Methods This study adopted the cross-sectional, contingent valuation study that involved 400 respondents in Penang, Malaysia. The double-bounded dichotomous choice via bidding game approach was employed to elicit the WTP value for two hypothetical 3-doses dengue vaccines (Vaccines A and B with 5- and 10-years’ protection, respectively against dengue). A univariate logistic regression model was employed to assess the key determinants of vaccine acceptance, while the mean WTP value and its associated factors were measured by using the parametric two-part model (TPM). Results Dengue vaccine appeared to be highly acceptable (88.4%) among the population in Penang, Malaysia. Respondents who were of Chinese ethnicity (OR 0.36, p = 0.017), with higher dengue knowledge score (OR 1.43, p = 0.016), and higher vaccination attitude score (OR 1.91, p < 0.001) were more likely to accept the vaccine. The first step logit estimation from TPM displayed that pensioners (OR 2.37, p = 0.036), respondents who were self-employed or working in the private sector (OR 1.21, p = 0.002), respondents with higher education level (OR 2.09–3.29, p < 0.05), and those who accepted the vaccine (OR 3.23, p = 0.001) were more likely to pay for the vaccine. The adjusted mean WTP value for the vaccine was MYR39.21 (USD9.45) per dose. Next, the second-stage regression from TPM revealed the key factors that significantly affected the WTP value, which were composed of age, gender, occupation, household income, dengue prevention practice, and protection duration of the vaccine. The pensioners and those with better dengue prevention practice were willing to pay more for the vaccines. Additionally, all the respondents elicited a higher WTP amount toward the vaccine with longer protection duration (Vaccine B). Conclusion Strong acceptance toward dengue vaccine reflects the high value of the vaccine in Malaysia. The WTP estimates offer quantification of the private benefit in reducing occurrences of the disease. Besides, the people’s preferences-based WTP value for the vaccine tends to complement scientific decision-making and prioritization in the management of dengue in the country. Electronic supplementary material The online version of this article (10.1186/s12962-018-0163-2) contains supplementary material, which is available to authorized users.