Abstract We established a proof-of-concept model system for the biological healing of periapical lesions using stem cell spheroids. Mesenchymal stem cells from human exfoliated deciduous teeth (SHED) were cultured in a 2D monolayer and then as 3D multicellular spheroids. An image of a periapical lesion of an upper lateral incisor tooth was obtained by computed tomography and was used as a model for photopolymer resin 3D printing to generate a negative frame of the lesion. The negative model served to prepare a positive model of the periapical lesion cavity in an agarose gel. SHED that were cultured in monolayers or as spheroids were seeded in the positive lesion mold before or after osteoblastic differentiation. The results showed that compared to cells cultured in monolayers, spheroids exhibited uniform cellularity and a greater viability within the lesion cavity, which was accompanied by a temporal reduction in the expression of CD13, CD29, CD44, CD73, and CD90 mRNAs that are typically expressed by stem cells. Concomitantly, the expression of markers that characterize osteoblastic differentiation (RUNX2, ALP, and BGLAP) increased. These results provide a new perspective for regenerative endodontics with the use of SHED-derived spheroids to repair periapical lesions.