Short-chain fructooligosaccharides (scFOS) in the maternal diet during gestation and lactation positively modulate gut microbiota and maturation of the intestinal immune system in the offspring. The effect of maternal and post-weaning scFOS supplementation on the efficiency of the humoral response to influenza vaccination was evaluated. Seventeen sows received a standard or a scFOS supplemented diet for the last 4 weeks of gestation and lactation. From weaning, 128 pigs were fed a standard or a scFOS supplemented diet for 7 weeks. Post-weaning scFOS diet increased anti-influenza IgA levels in pig serum and faeces whereas maternal scFOS supplementation moderated the decrease of piglet growth induced by sow seropositivity to influenza during lactation and further resulted in a higher body weight at 10 weeks of age. This study confirms a potential interest of early scFOS supplementation to enhance vaccine response and to promote growth.