ABSTRACT Aims To investigate the effects of Porphyromonas endodontalis on the viability of stem cells from the apical papilla (SCAP) and to explore the role of mitochondrial function in supporting SCAP survival. Methodology SCAP were isolated from immature third molars, and P. endodontalis was added to the cell culture medium. Cell proliferation and apoptosis were assessed using the CCK8 assay and flow cytometry, with vascular endothelial cells (VECs) serving as a comparative group. Transmission electron microscopy was utilised to observe the mitochondrial morphology and bacterial ultrastructure. Changes in mitochondrial membrane potential (MMP) were assessed using laser scanning confocal microscopy. Additionally, the effects of mitophagy or mitochondrial fission inhibitors on SCAP cell viability and MMP were evaluated. Transcriptomic high‐throughput sequencing was conducted to analyse differentially expressed mRNAs in SCAP and VECs after P. endodontalis infection using gene set enrichment analysis. Western blotting was performed to detect the expression of proteins associated with mitophagy and mitochondrial fission. The co‐localisation of microtubule‐associated protein light chain 3 with translocase of the outer mitochondrial membrane 20 (TOM20), as well as dynamin‐related protein 1 with TOM20, was examined using laser scanning confocal microscopy. Data were analysed using SPSS 22.0, and a p ‐value < 0.05 was considered statistically significant. Results Following 6 h of P. endodontalis infection, SCAP exhibited higher cell viability and lower cell apoptosis rates than VECs. In addition, SCAP maintained more stable mitochondrial morphology and higher MMP compared to VECs. Transcriptomic analysis revealed that differentially expressed mRNAs between infected SCAP and VECs were enriched in terms related to mitochondrial membrane, depolarisation and mitochondrial fission. P. endodontalis infection also upregulated the expression of proteins associated with mitophagy and mitochondrial fission in SCAP. Inhibition of either mitophagy or mitochondrial fission in SCAP decreased the viability of SCAP. Conclusions SCAP could maintain cell viability after short‐term P. endodontalis infection. The underlying mechanism may involve mitochondrial fission and mitophagy, which appear to function as key protective processes enabling SCAP to counteract infection‐induced cellular damage. This study helps elucidate the molecular basis of SCAP survival under bacterial infection.