•Equine-like G3P8 the major cause of gastroenteritis during RV3-BB efficacy trial.•The Indonesian equine-like G3P8 strain was genetically similar to Hungarian and Spanish strains.•Equine-like G3P8 strain is an emerging cause of gastroenteritis in Indonesia. The RV3-BB human neonatal rotavirus vaccine aims to provide protection from severe rotavirus disease from birth. The aim of the current study was to characterise the rotavirus strains causing gastroenteritis during the Indonesian Phase IIb efficacy trial. A randomized, double-blind placebo-controlled trial involving 1649 participants was conducted from January 2013 to July 2016 in Central Java and Yogyakarta, Indonesia. Participants received three doses of oral RV3-BB vaccine with the first dose given at 0–5 days after birth (neonatal schedule), or the first dose given at ∼8 weeks after birth (infant schedule), or placebo (placebo schedule). Stool samples from episodes of gastroenteritis were tested for rotavirus using EIA testing, positive samples were genotyped by RT-PCR. Full genome sequencing was performed on two representative rotavirus strains. There were 1110 episodes of acute gastroenteritis of any severity, 105 episodes were confirmed as rotavirus gastroenteritis by EIA testing. The most common genotype identified was G3P8 (90/105), the majority (52/56) of severe (Vesikari score ≥11) rotavirus gastroenteritis episodes were due to the G3P8 strain. Full genome analysis of two representative G3P8 samples demonstrated the strain was an inter-genogroup reassortant, containing an equine-like G3 VP7, P8 VP4 and a genogroup 2 backbone I2-R2-C2-M2-A2-N2-T2-E2-H2. The complete genome of the Indonesian equine-like G3P8 strain demonstrated highest genetic identity to G3P8 strains circulating in Hungary and Spain. The dominant circulating strain during the Indonesian Phase IIb efficacy trial of the RV3-BB vaccine was an equine-like G3P8 strain. The equine-like G3P8 strain is an emerging cause of severe gastroenteritis in Indonesia and in other regions.