The World Health Organisation recommends vitamin A supplementation (VAS) to children aged 6 months to 5 years in low-income countries, and for logistic reasons, this has been linked to routine childhood immunizations. Observational studies suggest that VAS given with diphtheria-tetanus-pertussis (DTP) vaccine may increase mortality from non-targeted diseases. We investigated the non-targeted effect of pretreatment with VAS and DTP vaccine in a murine model of experimental cerebral malaria. Our a priori hypothesis was that VAS/DTP would aggravate the infection. We found that the effect of VAS and DTP depended on pathogenesis; VAS/DTP tended to increase parasitaemia and significantly depressed cytokine responses in mice, which developed cerebral malaria, but this was not seen in mice dying of anaemia. The divergent effect according to pathogenesis may help elucidate why VAS has divergent effects on different diseases in humans. Our results support the hypothesis that immunological effects of VAS/DTP may have detrimental implications for disease outcomes.