We explored the association between baseline gut microbiota (16S rRNA biomarker sequencing of stool samples) in 17 relapsing-remitting pediatric MS cases and risk of relapse over a mean 19.8 months follow-up. From the Kaplan-Meier curve, 25% relapsed within an estimated 166 days from baseline. A shorter time to relapse was associated with Fusobacteria depletion (p = 0.001 log-rank test), expansion of the Firmicutes (p = 0.003), and presence of the Archaea Euryarchaeota (p = 0.037). After covariate adjustments for age and immunomodulatory drug exposure, only absence (vs. presence) of Fusobacteria was associated with relapse risk (hazard ratio = 3.2 (95% CI: 1.2-9.0), p = 0.024). Further investigation is warranted. Findings could offer new targets to alter the MS disease course.