Introduction: The aim of this systematic review is to analyse the effect of physico-chemical properties of calcium silicate-based sealers in comparison to epoxy resin sealers in permanent teeth using a single-cone obturation technique. Methods: The study was conducted according to the guidelines of Cochrane Handbook for Systematic Reviews of Interventions and Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) statement. Literature search was performed using the PubMed/MEDLINE, Cochrane Central Register of Controlled Trials, Web of Science, DOAJ, Open Gray with no language restrictions until October 2020. Two reviewers assessed the studies for eligibility. Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) was carried out to assess the evidence. Meta-analysis of the pooled data with subgroups was performed using the RevMan software (p < 0.05). Results: Results from the 28 included studies showed that the mean difference in adaptation to root canal walls (marginal adaptation, interfacial gaps and void volume) for both sealers were non-significant. However, void volume values showed a significant mean difference (p < 0.00001) favouring the calcium silicate-based sealers. The pooled meta-analysis reported statistically significant differences for apical microleakage (p = 0.0007) whilst there were non-significant mean differences for fracture resistance (p = 0.09) and push-out bond strength (p = 0.63). The heterogeneity among the included studies was 97% (I2). Conclusions: Within the limitations of this review, calcium silicate-based sealers demonstrated a similar or superior performance in comparison to resin-based sealers in terms of the physico-chemical properties.