Abstract Background/objectives Childhood rapid growth and earlier puberty onset have been associated with adult obesity. However, the association between childhood stunting, pubertal timing and adult obesity is unclear. We examined whether the relationship between stunting at age 2 years (y) and body composition at 23 years is mediated by adolescent body mass index, and pubertal development, using the Birth-to-Twenty Plus cohort (South Africa). Subjects/methods For 1036 participants, data on anthropometrics between birth and 23 years, maternal factors, and pubertal development (Tanner scale at 9–16 years) were collected. Stunting at 2 years (height-for-age z-score < −2), 5–18 years BMI-for-age trajectories, pubertal development trajectories, and DXA-derived fat mass (FM) and fat free mass (FFM) at 23 years were determined. Data were analysed using hierarchical regressions and structural equation models. Results Stunting was directly associated with slower pubertal development and with shorter adult stature, but was not associated with adolescent BMI trajectories, adult FM or FFM. However, stunting was indirectly associated with adult FM and FFM through the direct associations between slower pubertal development and lower FM and between shorter height and lower FFM. BMI trajectories were independently associated with FM and FFM. Conclusions Being stunted in this population predicted adult body composition through slower pubertal development and shorter adult stature.