Background: The oral and dental infections that are mainly caused by bacterial biofilms are among the most prevalent human infections worldwide. Objectives: The present study aimed to investigate the in vitro and in vivo inhibitory and anti-biofilm effects of oregano essential oil on the Streptococcus mutans isolates obtained from elementary school students. Methods: This experimental study was conducted on 150 samples collected from the buccal and lingual surfaces of the posterior teeth of elementary school students. S. mutans strains were identified using conventional microbiological and biochemical tests, and biofilm formation was assessed using the microtiter plate assay. The minimum inhibitory concentration (MIC) of the oregano essential oil against the isolates was determined using the broth microdilution method. In addition, the effective constituents of the essential oil were measured via gas chromatography-mass spectroscopy. The in vitro and in vivo anti-biofilm activities of the oregano essential oil were also evaluated using the modified microtiter plate assay and on the tooth surfaces of male NMRI mice, respectively. Results: The frequency of S. mutans was 15.3%, 87% of which were capable of biofilm formation. The MIC of the oregano essential oil was 50 µl/ml against the S. mutans isolates, and 82% of the isolates did not grow at the concentrations of ≥ 512 µl/ml. However, none of the isolates were capable of biofilm formation at the MIC and sub-MIC concentrations of the essential oil. Limonene and myrcene were the most effective constituents of the essential oil. Furthermore, a significant correlation was observed between treatment with the oregano essential oil and biofilm formation by the streptococci isolates (P = 0.05). Conclusions: According to the results, the presence of biofilm and incidence of dental caries were significantly correlated. Moreover, the essential oil of oregano and its main constituents had potent anti-biofilm and antibacterial properties and could be utilized for the production of new plant-based mouthwashes.