This systematic review aimed to evaluate the cytotoxicity of intracanal medicaments used for root canal disinfection and assess their effect on the proliferation and differentiation potential of stem cells from apical papilla (SCAP). The PubMed/Medline, Cochrane, Scopus, EMBASE, CINAHL and Web of Science databases were searched. Studies evaluating the effect of intracanal medicament on human SCAP (in-vitro primary cell culture experiment) were included in this systematic review. The risk of bias analysis of included studies was carried out using the Toxicological data Reliability Assessment tool. The data was analysed for qualitative characteristics. A meta-analysis was not carried out considering the heterogeneity of selected studies in terms of cell culture experiments, methods of analysis and the interpretation of results. Four studies fulfilled the desired inclusion criteria. The different antibiotic pastes and their intracanal concentrations lead to reduction in the SCAP survival compared to calcium hydroxide medicament. The findings were insufficient to make a clear distinction between different antibiotic pastes regarding their cytotoxicity. Within the limitations of the present systematic review, it can be concluded that calcium hydroxide is a relatively better intracanal medicament than antibiotic paste mixtures in terms of their cytotoxicity and effect on proliferation of SCAP.