A root canal sealer with antibacterial activity can be efficacious in preventing reinfection that results from residual microorganisms and/or the leakage of microorganisms. In the present study, a series of injectable, self-curing polyurethane (PU)-based antibacterial sealers with different concentrations of silver phosphate (Ag
3
PO
4
) were fabricated. Subsequently, their physicochemical properties, antibacterial abilities, and preliminary cytocompatibilities were evaluated. The results indicated that the fabricated PU-based sealers can achieve a high conversion rate in a short amount of time. More than 95% of the isocyanate group of PU sealers with 3 wt% (PU3) and 5 wt% (PU5) concentrations of Ag
3
PO
4
were included in the curing reaction after 7 hours. With the exception of those for film thickness for PU5, the results of setting time, film thickness, and solubility were able to meet the requirements of the International Organization for Standardization. The antibacterial tests showed that PU3 and PU5 exhibit stronger antimicrobial effects than that achieved with 1 wt% Ag
3
PO
4
(PU1) and AH Plus (positive control) against
Streptococcus mutans
. The cytocompatibility evaluation revealed that the PU1 and PU3 sealers possess good cytocompatibility and low cytotoxicity. These results demonstrate that the PU3 sealer offers good physicochemical and antimicrobial properties along with cytocompatibility, which may hold great application potential in the field of root canal fillings.