This article addresses three main issues: the relationship between commute time and sickness absence, the heterogeneity of the commuting–absenteeism effect between rural migrants and urban citizens, and the effect of China’s Hukou system on the commuting–absenteeism effect. It applies a unique set of employer–employee matched data in China and a zero-inflated negative binomial model. We find clear evidence that a longer commuting time contributes to an increase in sickness absence. The heterogeneity of the commuting–absenteeism effect can also be confirmed: longer commuting leads to higher absence rates for urban citizens but not for rural migrants. Furthermore, we explore the effect of commuting on a set of health-related outcomes. The estimations demonstrate that commuting time has a significant impact on health-related outcomes for both migrants and urban citizens, but unequal access to housing provision and to social health insurance in the Hukou system may mean that rural migrants resort to more informal medical services and thus lack access to the official sickness certificate required to seek legal sickness absence. We recommend accelerated reform of the Hukou system to encourage rural workers to seek appropriate and timely medical services, thereby reducing public health risks.