Functional abdominal pain disorders (FAPDs) are common in children and are associated with alterations in the gut-brain axis and intestinal microbiota. Although individual probiotic strains such as Limosilactobacillus reuteri DSM 17938 and Lacticaseibacillus rhamnosus GG have demonstrated efficacy over placebo, direct comparative evidence between strains is limited. This prospective quasi-experimental analysis with blinded outcome assessment was conducted at a tertiary care centre in South India between January 2025 and March 2026. Children aged 5-12 years diagnosed with Functional Abdominal Pain-Not Otherwise Specified (FAP-NOS) according to Rome IV criteria were randomised (1:1) to receive either L. reuteri DSM 17938 or L. rhamnosus GG for two months. The primary outcome was reduction in monthly pain frequency at two months. Secondary outcomes included reduction in pain intensity and school absenteeism with a six-month follow-up. A total of 124 children were randomised, with 100 completing the study per protocol. Both groups showed significant reductions in pain frequency from baseline to two months (P-value < 0.001). Median pain frequency decreased from 5.00 to 2.00 episodes/month in the L. reuteri group and from 6.00 to 1.00 in the L. rhamnosus group, with no significant between-group difference (P-value = 0.784). Pain intensity and school absenteeism also significantly decreased within groups without intergroup difference. Improvements were sustained at six-month follow-up. Both L. reuteri DSM 17938 and L. rhamnosus GG demonstrate comparable effectiveness in reducing pain frequency, pain intensity and school absenteeism in children with FAP-NOS, with sustained benefits. The trial is registered at Clinical Trials Registry-India under CTRI/2025/01/079050.
