The aim of this study was to evaluate the biocompatibility of calcium silicate-based sealers (CeraSeal and EndoSeal TCS) and epoxy resin-based sealer (AH-Plus) in terms of cell viability, inflammatory response, expression of mesenchymal phenotype, osteogenic potential, cell attachment, and morphology, of human periodontal ligament stem cells (hPDLSCs). hPDLSCs were acquired from the premolars (n = 4) of four subjects, whose ages extended from 16 to 24 years of age. Flow cytometry analysis showed stemness of hPDLSCs was maintained in all materials. In cell viability test, AH-Plus showed the lowest cell viability, and CeraSeal showed significantly higher cell viability than others. In ELISA test, AH-Plus showed higher expression of IL-6 and IL-8 than calcium silicate-based sealers. In an osteogenic potential test, AH-Plus showed a lower expression level than other material; however, EndoSeal TCS showed a better expression level than others. All experiments were repeated at least three times per cell line. Scanning electronic microscopy studies showed low degree of cell proliferation on AH-Plus, and high degree of cell proliferation on calcium silicate-based sealers. In this study, calcium silicate-based sealers appear to be more biocompatible and less cytotoxic than epoxy-resin based sealers.