Unlike milk-based infant formulas, soy-based infant formulas containing supplemental fructooligosaccharides (FOS) have not been clinically evaluated. A randomized, double-blind, 28 day parallel feeding trial compared gastrointestinal (GI) tolerance and hydration in healthy term newborn infants fed either a commercialized soy formula (with history of safe use) containing sucrose as 20% of total carbohydrate, no supplemental short-chain FOS (scFOS) and no mixed carotenoids (lutein, lycopene, beta-carotene) as a control (CF, n = 62 infants) or one of two experimental soy-based formulas, EF1 (n = 64) and EF2 (n = 62) containing scFOS (2.5 g/L) and mixed carotenoids. EF1 differed from EF2 by containing sucrose. Results indicated no significant study group differences (p > 0.05) in study completion rates (CF = 81, EF1 = 86, & EF2 = 87%), growth, mean rank stool consistency, stool frequency, formula intake, spit-up/vomit, and safety measures (urine specific gravity, USG; hydration status and adverse events). Mean USGs for study groups were normal (<1.03). The EF1 > CF group in percent yellow stools (p < 0.01 at age 14 days). In conclusion, the study suggested that term infants fed soy-based formulas supplemented with scFOS and mixed carotenoids, with or without sucrose in the 1st 35 days of infancy demonstrated good tolerance and hydration comparable to the control soy-based formula with history of safe use.