Streptococcus gordonii, a bacterium involved in the initial colonization of tooth surfaces, contributes to dental biofilm formation and is an important cause of infective endocarditis. This study aimed to investigate the influence of surface reaction-type pre-reacted glass ionomer (S-PRG) filler on oral bacterial growth and aggregation of S. gordonii. The effect of various concentrations of S-PRG eluate on the growth and the biofilm formation of S. gordonii and other oral microorganisms (Streptococcus mutans, Streptococcus oralis, Lactobacillus acidophilus, and Candida albicans) was assessed. In addition, the effect of S-PRG eluate on coaggregation of S. gordonii with both S. oralis and Fusobacterium nucleatum was assessed. The effect of S-PRG eluate treatment on autoaggregation of S. gordonii was also evaluated. Our results indicate that S-PRG eluate treatment reduced both for the growth and for biofilm of all organisms in a dose-dependent manner. Coaggregation of S. gordonii with both S. oralis and F. nucleatum was inhibited by S-PRG eluate, whereas autoaggregation of S. gordonii increased at certain concentrations of S-PRG eluate. These results indicate that the S-PRG filler possesses antimicrobial activity that is mediated by inhibiting growth and biofilm of oral microorganisms, and by suppressing coaggregation of S. gordonii. In addition, these findings indicate that coaggregation of S. gordonii with other bacteria is inhibited by increased autoaggregation of S. gordonii.