Surface pre-reacted glass-ionomer (S-PRG) filler releases several ions, such as fluoride, borate and strontium ions, to exert bioactive effects. We fabricated an endodontic root canal sealer containing S-PRG fillers (S-PRG sealer) and then evaluated the antibacterial and anti-inflammatory properties of S-PRG sealer compared with sealer containing conventional silica fillers (silica sealer). Antibacterial tests showed that S-PRG sealer significantly reduced the turbidity of Enterococcus faecalis compared with silica sealer. Implantation of S-PRG or silica sealer blocks in rat subcutaneous tissue showed that S-PRG sealer decreased the proinflammatory response compared with silica sealer at 10 days post-implantation. In addition, immunostaining revealed that infiltration of CD68- and peroxidase-positive cells around the S-PRG sealer was significantly lower than that in silica sealer. Therefore, it was suggested that S-PRG sealer exhibits antibacterial and anti-inflammatory effects.