With labor being a central social determinant of health, there is an increasing need to investigate health inequalities within the heterogenous and growing population in self-employment. This study aimed to longitudinally investigate the relationship between income level, self-employment status and multiple work-related health indicators in a Swedish national cohort (n = 3,530,309). The study investigated the relationship between self-employment status and health outcomes later in life. All poor health outcomes, with the exception of alcohol-related disorders, were more common in the self-employed population, compared to the group in regular employment. The income gradient, however, was more pronounced in the group with regular employment than the groups in self-employment. The study found clear connections between low income and poor health in all employment groups, but the gradient was more pronounced in the group in regular employment. This suggests that income has a weaker connection to other types of health promoting resources in the self-employed population. Potentially, lacking social and public support could make it difficult for unhealthy individuals to maintain low-income self-employment over a longer time period.