AimWe examined the effects on gastrointestinal (GI) tolerance of a novel infant formula that combined specific fermented formula (FERM) with short‐chain galacto‐oligosaccharides and long‐chain fructo‐oligosaccharides (scGOS/lcFOS), with a 9:1 ratio and concentration of 0.8 g/100 mL.MethodsThis prospective, double‐blind, randomised, controlled trial comprised 432 healthy, term infants aged 0–28 days whose parents decided to not start, or discontinued, breastfeeding. Infant formula with scGOS/lcFOS+50%FERM, scGOS/lcFOS+15%FERM, 50%FERM and scGOS/lcFOS were tested. Parents completed standardised seven‐day diaries on GI symptoms, crying, sleeping and stool characteristics each month until the infants were 17 weeks.ResultsAll the formulas were well tolerated. At four weeks, the overall incidence of infantile colic was significantly lower (8%) with scGOS/lcFOS+50%FERM than scGOS/lcFOS (20%, p = 0.034) or 50%FERM (20%, p = 0.036). Longitudinal modelling showed that scGOS/lcFOS+50%FERM‐fed infants also displayed a persistently lower daily crying duration and showed a consistent stool‐softening effect than infants who received formula without scGOS/lcFOS.ConclusionThe combination of fermented formula with scGOS/lcFOS was well tolerated and showed a lower overall crying time, a lower incidence of infantile colic and a stool‐softening effect in healthy term infants. These findings suggest for the first time that a specific infant formula has a preventive effect on infantile colic in formula‐fed infants.