The purpose of the present study was to evaluate the mechanical and chemical properties of a novel glass ionomer cement for use as a pit and fissure sealant containing a porous hydroxyapatite, namely, apatite ionomer cement (AIC). Control sealant samples were used Fuji III (GIC-S). The experiment sealant samples (AIC-S) consisted of porous spherical hydroxyapatite (HApS) particles added at 28 wt% to GIC-S powder. The GIC-S and AIC-S samples were evaluated through mechanical strength measurements, scanning electron microscopy observations, energy dispersive X-ray spectroscopy analysis, fluoride ion release tests, and antibacterial tests. The flexural strength of the AIC-S was significantly higher than that of GIC-S for each period, 1 h, 24 h and 1 year. The fluoride release dose for AIC-S was consistently higher than that for GIC-S. In addition, the antibacterial properties of AIC-S were superior to those of GIC-S. The novel AIC-S may be a more suitable sealant material for pits and fissures with intact and/or infected enamel.