Papillary thyroid carcinoma (PTC) accounts for approximately 80% of total thyroid cancer worldwide. Although the prognosis for early-stage PTC is favorable, the 5-year survival rate of patients with late-stage PTC is still very poor. Cystatin SN (cystatin 1, CST1) facilitates the progression of multiple cancers, but its role in regulating papillary thyroid carcinoma (PTC) pathogenesis is still largely unknown. In the present study, we measured the expression levels of CST1 in PTC clinical tissues and cell lines by real-time qPCR and western blot analysis, and performed gain-and loss-of-function experiments to examine the effects of CST1 on PTC cell growth, invasion, migration, epithelial-mesenchymal transition (EMT) and stemness.Tumorigenicity was assessed using in vivo tumor-bearing nude mice models. As expected, upregulated CST1 was observed in PTC tissues (P < 0.05) and cells, compared to their normal counterparts (P < 0.05); furthermore, PTC patients with higher levels of CST1 exhibited unfavorable prognosis (P < 0.05). In addition, CST1 ablation inhibited PTC cell growth (P < 0.05) in vivo and in vitro. Silencing of CST1 also inhibited cell motility and EMT in PTC cells (P < 0.05), while CST1 overexpression had the opposite effects on the above cellular functions. Of note, upregulation of CST1 promoted cell spheroid formation (P < 0.05) and increased the expression levels of stemness signatures (P < 0.05) in PTC cells. Collectively, these findings suggest that CST1 functions as an oncogene to facilitate cancer development and promote cancer stem cell (CSC) properties in PTC cells, increasing our understanding of PTC pathogenesis mechanisms and possibly aiding in the development of potential therapeutic strategies.