Objective: To explore the effects of Sirtuin 7 (SIRT7) on the gene expression profile of stem cells from the apical papilla (SCAPs). Methods: SCAPs were isolated and cultured. SIRT7 short hairpin ribonucleic acid (shRNA) was used to knock down the expression of SIRT7 in SCAPs. After library construction and RNA sequencing (RNA-seq), differentially expressed genes were identified using Cuffdiff with a false discovery rate (FDR) ≤ 0.05 and fold change ≥ 2. Pathway and Gene Ontology (GO) analyses were conducted to elucidate the changes in important functions and pathways after SIRT7 gene knockdown. Gene set enrichment analysis (GSEA) was performed and enrichment of a gene set with an FDR lower than 0.25 was considered significant. Results: The most striking GO terms related to SIRT7sh SCAPs and Consh SCAPs were response to nucleus, nucleolus, cytoplasm, protein binding and intrinsic apoptotic signalling pathway. Signalling pathway analysis revealed the top five pathways to be metabolic, pyrimidine metabolism, protein processing in endoplasmic reticulum, phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signalling and p53 signalling. The results of GSEA showed that genes were mainly enriched in cell cycle, cell proliferation, transforming growth factor beta (TGF-β) signalling and cytokine–cytokine receptor interaction pathways. Conclusion: SIRT7 may affect the functions of SCAPs through cell cycle, cell proliferation and apoptosis pathways. Keywords: RNA sequencing, SIRT7, stem cells from the apical papilla