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One of the targets in the Sustainable Development Goals (SDGs), which is Target 6.2, aims to achieve access to adequate and equitable sanitation. The Government of Indonesia targets universal access to improved sanitation in 2019. However, almost two out of five households in Indonesia are without access to improved sanitation. Moreover, access to improved sanitation is lower in rural areas than that in urban areas. Studies examining the drivers of the disparity in Indonesia are also limited. Therefore, this study was aimed at assessing the characteristics associated with the rural–urban disparity in access to improved sanitation facilities among households in Indonesia. We employed data from the 2016 Indonesian National Socio-Economic Survey (SUSENAS) comprising 290,848 households. The analysis was twofold. First, we fitted multivariate probit regression models using average marginal effects as the measure of association. We then conducted a detailed non-linear decomposition of the rural–urban disparity attributable to all the explanatory variables. The multivariate regression analysis suggested that households living in rural areas were 11.35% (95% confidence interval = [10.97, 11.72]) less likely to have access to improved sanitation facilities than those residing in urban areas. The decomposition analysis suggested that 48.78% are attributable to spatial, demographic, housing, and socio-economic factors, which meant that almost half of the inequalities could be reduced by equalizing these factors. The results provide a decomposition of factors amenable to curtail urban–rural inequalities. Hence, equity-oriented approaches to increasing access to improved sanitation should be prioritized to achieve universal access in 2030 in line with SDG Target 6.2.

Rural–Urban Disparities in Access to Improved Sanitation in Indonesia: A Decomposition Approach