Research has demonstrated the need for identifying a novel antimicrobial agent for topical use in the pediatric dental population. The essential oil of Lippia sidoides Cham. (LSO) has been described as having favorable biological properties, and a broad in vitro and in vivo antimicrobial spectrum against bacteria and yeast infections. Our aim was to determine a dose and formulation of LSO, acceptable for clinical testing in a pediatric population with dental caries. Thirty-seven 6-12-year old children were selected to participate in this study, and randomly allocated to receive different concentrations of either a gel (0.8%, 1%, 1.2% and 1.4%) or a mouth rinse (0.6%, 0.8%, 1% and 1.2%) formulation. The highest percentage MS reduction was observed with 0.8% mouth rinse and 1.4% gel. The efficacy of these concentrations was compared with a Thy-Car mixture formulated as a mouth rinse and gel treatments in 11 children. Saliva was collected after a single application of the antimicrobial treatment to establish effectiveness against MS. Both rinse (p<0.001) and gel (p=0.02) formulations produced significant MS reduction. Mouth rinse concentrations above 0.8% were associated with a transient intra-oral burning sensation. In conclusion, mouth rinse and gel LSO formulations demonstrated effectiveness against MS and good acceptance among children. We suggest future randomized clinical trials to test its effectiveness against early childhood caries.