Background: Despite the greater attention given to international migration, internal migration accounts for the majority of movements globally. However, research on the effects of internal migration on health is limited, with this relationship examined predominantly in urban settings among working-age adults, neglecting rural populations and younger and older ages. Objectives: Using longitudinal data from 29 mostly rural sub-Saharan African Health and Demographic Surveillance Systems (HDSS), this study aims to explore life-course differences in mortality according to migration status and duration of residence. MethodsCox proportional hazards models are employed to analyse the relationship between migration and mortality in the 29 HDSS areas. The analytical sample includes 3 836,173 people and the analysis spans 25 years, from 1990 to 2015. We examine the risk of death by sex across five broad age groups (from ages 1 to 80), and consider recent and past in- and return migrants. Results: In-migrants have a higher risk of mortality compared to permanent rural residents, with return migrants at greater risk than in-migrants across all age-groups. Female migrants have lower survival chances than males, with greater variability by age. Risk of dying is highest among recent return migrant females aged 30–59: 1.86 (95% CI 1.69–2.06) times that of permanent residents. Only among males aged 15–29 who move to urban areas is there evidence of a ‘healthy migrant’ effect (HR = 0.62, 95% CI 0.51–0.77). There is clear evidence of an adaptation effect across all ages, with the risk of mortality reducing with duration following migration. Conclusions: Findings suggest that adult internal migrants, particularly females, suffer greater health disadvantages associated with migration. Policy makers should focus on improving migrant’s interface with health services, and support the development of health education and promotion interventions to create awareness of localised health risks for migrants