Health inequalities are generated by the conditions in which people are born, grow, live, work and age. From a life-course perspective, these conditions are formed by complex causal relationships with mutual and intertwined paths between socioeconomic position and health. This study attempts to disentangle some of these processes by examining pathways between socioeconomic position and health across the life-course. We used yearly Swedish national register data with information from over 31 years for two cohorts born 1941-1945 and 1961-1965. We analyzed associations between several indicators of childhood and adult socioeconomic position and health, measured by number of in-patient hospitalizations. We estimated within- and between-person associations using random intercept cross-lagged panel models. The results showed bi-directional associations between socioeconomic position and health that varied in strength across the life-course. Age variations in the associations were primarily observed when individuals aged into or out of age-stratified institutions. In ages where transitions from education to the labor market are common, the associations from health to income and education were strong. Around and after retirement age, the between-person association from health to income was weak, while the association from income to health strengthened. Within-person estimates showed no association between income and subsequent hospitalization among older persons, indicating no direct causal effect of income change on health in this age group. For persons of middle age, the associations were of similar strength in both directions and present at both the between- and within-person level. Our findings highlight the importance of theoretical frameworks and methods that can incorporate the interplay between social, economic, and biological processes over the life-course in order to understand how health inequalities are generated.