D-Allulose, a low-calorie sugar, provides an attractive alternative to added sugars in food and beverage products. There is however limited data on its gastrointestinal (GI) tolerance, with only two studies in adults, and no studies in children to date. We therefore performed an acute, randomised, double-blind, placebo-controlled, cross over study designed to determine, for the first time, the GI tolerance of 2 doses of D-allulose (2.5 g per 120 ml and 4.3 g per 120 ml) in young children. The primary tolerance endpoint was the difference in the number of participants experiencing at least one stool that met a Type 6 or Type 7 description on the Bristol Stool Chart, within 24 hours after study product intake. Secondary endpoints included the assessment of stool frequency, stool consistency, and the presence of GI symptoms. Only one participant in the low dose group experienced a stool type 6 or 7, while no participants experienced a stool type 6 or 7 in the high dose group. A statistically significant difference in the change in stool frequency compared to placebo in the high dose group (p = 0.044) was found, with no significant difference between the groups for stool consistency and no participants experienced unusual stool frequency. All the encountered adverse events were non-serious, either mild or moderate, and there were no serious adverse events. All in all, D-allulose was tolerated well in children, making this ingredient a good candidate to reformulate commercially produced goods by replacing added sugars with lower caloric content.