Improved drinking-water sources need not be microbiologically safe. Hence, households usually boil their water prior to drinking. However, this practice can potentially harm health when households rely on unsafe cooking fuels. In Indonesia, little is known about the association of use of unsafe fuels with boiling practice. Hence, an analysis was carried out to elicit information regarding boiling practice using unsafe fuels. Such information would be useful in determining appropriate household water treatments. Data from the 2012 Indonesia Demographic and Health Survey (IDHS) were analysed to examine the relationship between the use of unsafe cooking fuel and choosing boiling as household water treatment. Bivariate and multivariate probit regression models (PRM) were fitted and compared using average marginal effects (AME) and its respective 95 per cent confidence interval (95% CI) as measures of association. The results suggest that using kerosene as cooking fuel is positively significantly associated with higher probability of practicing boiling (p = 0.006; 0.019; 95% CI: 0.0056, 0.0333). This is also true for use of solid fuel (p< 0.001; AME: 0.3115; 95% CI: 0.3026, 0.3203). These association holds, albeit attenuated (Kerosene, p< 0.001; AME: 0.02706; 95% CI: 0.0186, 0.0355; Solid fuel, p< 0.001; AME: 0.0373; 95% CI: 0.02839, 0.0463), after the control variables are included. The authors suggest that stakeholders should promote the use of other household water treatment technologies to reduce the boiling practice using unsafe cooking fuels as to minimize the risk of smoke related infections. Moreover, universal access and equity to safe drinking water and sanitation facility in Indonesia should be realised to reduce demand of boiling water using unsafe cooking fuels.