The purpose of this study was to assess the effect of a calcium silicate-based sealers (CeraSeal) and an epoxy resin-based sealer (AH Plus) on cytotoxicity and cell migration of stem cell from the human apical papilla (hSCAPs) by using the Alamar Blue, Annexin V-FICT and wound healing assays. In Alamar Blue assay, hSCAPs exposed to undiluted CeraSeal extract had significantly higher cell viability compared with that observed when cells were treated with AH Plus in all experimental period (p < 0.001). The flow cytometry analysis confirmed the comparison on viable cells and indicated that AH Plus increased apoptosis compared to CeraSeal and the control groups (p < 0.001). Additionally, AH Plus exhibited significantly lower level of cell migration than CeraSeal and the control for up to 48 h observation (p < 0.01). In summary, calcium silicate-based sealer (CeraSeal) is less cytotoxic and more biocompatible than epoxy resin-based sealer (AH Plus).