Background: Worldwide, Streptococcus pyogenes is the leading cause of bacterial pharyngitis. To reduce the use of antibiotics, antimicrobial phytochemical-containing remedies, which have long been in use in traditional medicine, may provide new approaches for management of streptococcal pharyngitis. The objective of this study was to assess the inhibitory activities of 25 natural phenolic compounds against three strains of S. pyogenes. Methods: After an initial screening, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the nine most effective phenolic compounds were determined. The effect of four compounds with the lowest MIC and MBC on streptococcal growth and biofilm formation was also studied. Results: 1,2-Naphthoquinone and 5-hydroxy-1,4-naphthoquinone elicited the greatest anti-S. pyogenes activities with MICs ranging from 0.39 to 6.25 µg mL−1 and MBCs of 100 µg mL−1. Both naphthoquinones inhibited the biofilm formation at concentrations ranging from 12.5 to 50 µg mL−1. Biofilm reduction and altered bacterial cell structures were visible in scanning electron microscopy images of naphthoquinone-treated cells. Conclusion: In conclusion, 1,2-naphthoquinone and 5-hydroxy-1,4-naphthoquinone inhibit S. pyogenes and should be further investigated as candidates for the management of streptococcal pharyngitis.