Aim To evaluate the expression of Foxp3‐positive lymphocytes around newly formed tissue after regenerative endodontic treatment (RET) in vivo and investigate the effects of stem cells from the apical papilla (SCAP) on the conversion of CD4+CD25− T cells to CD4+CD25+Foxp3+ regulatory T cells (Tregs) in vitro. Methodology Three 6‐month‐old beagles with nine doubled‐rooted premolars in each dog were randomly assigned to the RET group and the control group. RET was performed after apical periodontitis had been induced in the experimental immature teeth. Three months later, the expression of Foxp3 was detected in the histological sections by immunofluorescent staining. Human SCAP and CD4+CD25− T cells from mice spleens (1 : 1 and 1 : 5) were co‐cultured in cell–cell contact or in Transwells, respectively, for 24 and 72 h in vitro. The percentage of Tregs was evaluated by flow cytometry. The results were analysed using the Fisher's exact test and analysis of variance. P < 0.05 was regarded as statistically significant. Results Inflammatory cells were present with tissue regeneration in the RET group, and Foxp3‐positive T cells were enriched around the newly formed tissues. SCAP promoted Treg conversion after 72 h in vitro. Cell–cell contact played an important role after the 24 h co‐culture, whilst soluble factors were also involved after 72 h (P < 0.05). Conclusions SCAP promoted the conversion of pro‐inflammatory T cells to Tregs in vitro. Tregs were enriched around the regenerating tissues in the root canals after RET, which may create a suitable immune microenvironment for the differentiation of SCAP. This study provides an underlying mechanism for tissue regeneration during RET.