<b><i>Introduction:</i></b> The oral cavity is home to a diverse and distinct microbiome. While the role of oral bacteria in cariogenic and other dental diseases is irrefutable, their beneficial effects in the form of probiotics (PB) has been less studied, especially pertaining to oral diseases in children. This study compares the efficacy of a PB mouthrinse with 0.12% chlorhexidine (CHX) and 0.05% sodium fluoride (NaF) mouthrinse on the colony counts of mutans streptococci (MS) in children. <b><i>Methods:</i></b> A triple-blind crossover randomized trial between interventional groups was planned. Fifty-one children between 8 to 12 years of age were divided into three groups (I, II, and III) and were exposed to all three mouthrinses (A, B, and C) by randomized allocation for a period of two weeks with an inter-phase washout period of four weeks. Pre- and post-interventional MS counts (CFU/mL) were assessed, and the mean change was analysed using the <i>t</i> test (intragroup) and ANOVA (intergroup and crossover). <b><i>Results:</i></b> The mean changes in the colony counts obtained with the use of PB, CHX, and NaF mouthrinses were −1.0223 (−1.2201 to −0.8246), −0.9564 (−1.1503 to −0.7626), and −0.9511 (−1.1554 to −0.7467), respectively, which were statistically significant (<i>p</i> < 0.0001). However, the intergroup comparison for the mean change in colony counts revealed no statistically significant differences (<i>p</i> > 0.05). <b><i>Conclusion:</i></b> The study concluded that the PB mouthrinse was equally efficacious as compared to CHX and NaF mouthrinses against MS in 8- to 12-year-old children. However, further studies are recommended to strengthen the evidence.