Johnson is a Research Affiliate of Harvard's W.E.B. Du Bois Institute and the National Poverty Center. As a labor and health economist, his work considers the role of poverty and inequality in affecting life chances. He has focused on such topics as the long-run impacts of school quality on educational attainment and socioeconomic success, including the effects of desegregation, school finance reform, and Head Start. He has investigated the determinants of intergenerational mobility; the societal consequences of incarceration; effects of maternal employment patterns on child well-being; and the socioeconomic determinants of health disparities over the life course, including the roles of childhood neighborhood conditions and residential segregation.