While dietary fiber has been shown to influence the composition of gut microbiota and cognitive function in adults, much less is known about the fiber-microbiome-cognition association in children. We profiled gut microbiota using quantitative PCR (qPCR) and evaluated cognitive function using the Corsi block-tapping test (CBT) and the psychomotor vigilance test (PVT) before, during, and after the dietary intervention of 127 school-aged children in northern Thailand. While we found that Sinlek rice (SLR) consumption did not significantly alter the abundance of gut microbiota or the cognitive performance of school-aged children, we did find age to be associated with variations in both the gut microbiota profiles and cognitive outcomes. Gammaproteobacteria was significantly lower in the control and SLR groups during the middle time points of both phases (Weeks 4 and 61), and its abundance was associated with age. Cognitive performance using CBT and PVT were also found to be age-sensitive, as older children outperformed younger children on both of these cognitive assessments. Finally, a multiple factor analysis (MFA) revealed that age and cognitive performance best explain individual variation in this study. Collectively, these findings further describe the influence of host variables on the microbial profiles and cognitive outcomes of school-aged children consuming Sinlek rice in Thailand.