Tissue regeneration requires an interaction of stem cells and growth factors in a bioactive scaffold. This study utilized the ferret canine as an in situ animal model to investigate a clinically applicable tissue engineering approach for dentin-pulp regeneration. Specifically, we aimed to determine the efficacy of delivering stem cells within a bioactive scaffold directly into the root canal space, in the presence of growth factors released from dentin, compared with traditional procedures in dentin-pulp regeneration. Periapical lesions were induced in 24 canine teeth of 6 ferrets. Dental pulp stem cells were isolated, characterized, encapsulated in a hydrogel scaffold, and injected in half the experimental teeth. The other half were treated using the conventional protocol with a blood clot scaffold. After an evaluation period of 3 months, the animals were sacrificed and block sections were processed for radiographic analysis. Results showed that there was no statistically significant difference between groups. Some teeth in both groups showed control of the infectious process with increase in root wall thickness, root length and apical closure, while others did not. There was a significant association between the presence or absence of a periapical lesion at the 3-month evaluation and whether the tooth showed continued root maturation. Pre-operative infection may have played a critical role in the treatment outcome.