BACKGROUND: Bacillus Calmette-Guerin (BCG) vaccination possesses effects on health beyond its target disease, the so called "non-specific effects". We evaluate these effects, as well as the effect of timing of BCG and other vaccinations, on stunting in Sub-Saharan African (SSA) children under five. METHODS: We use a Big Data design, including cross-sectional data for 368,450 children from 33 SSA countries. Logistic regression analysis is used with control factors at child, mother, household and context level. RESULTS: Overall, BCG vaccination did not affect stunting in SSA children (OR 1.00 [0.98-1.03]). Timing of BCG vaccination was of importance (betatime=0.067 [0.061-0.073]): compared to unvaccinated children, BCG was associated with lower odds on stunting for children vaccinated early in life (OR 0.92 [0.89-0.94]) and higher odds for children vaccinated later in infancy (OR 1.64 [1.53-1.76]). Similar findings were done for diphtheria-tetanus-pertussis (DTP)1 and measles vaccination, and when hemoglobin concentration was used as outcome variable. CONCLUSIONS: We found a general time-dependent pattern of non-specific effects of vaccination, with positive associations for vaccinations given early in life and negative associations for vaccinations given later in infancy. If confirmed in further research, our findings may provide a new perspective on the non-specific effects of vaccination.