Up-regulation of lncRNA POU3F3 has been observed in esophageal squamous cell carcinomas, while its expression pattern and functionality in other human disease is unknown. Our study showed that plasma levels of lncRNA POU3F3 and TGF-β1 (transforming growth factor-β) were both increased in nasopharyngeal carcinoma patients than in healthy controls. Plasma levels of lncRNA POU3F3 were not affected by the diameter of primary tumors but increased in patients with tumor metastasis. Plasma levels of lncRNA POU3F3 and TGF-β1 were positively correlated only in nasopharyngeal carcinoma patients but not in healthy controls. Follow-up study showed that high plasma levels of lncRNA POU3F3 were significantly correlated with poor overall survival. LncRNA POU3F3 overexpression and exogenous TGF-β1 treatment led to promoted, while TGF-β1 inhibitor led to inhibited migration and invasion of nasopharyngeal carcinoma cells. TGF-β1 inhibitor partially rescued the inhibited cancer cell migration and invasion caused by lncRNA POU3F3 overexpression. LncRNA POU3F3 overexpression led to down-regulated TGF-β1 expression, while exogenous TGF-β1 and TGF-β1 inhibitor treatment did not significantly change the expression level of lncRNA POU3F3. Therefore, lncRNA POU3F3 may promote cancer cell migration and invasion in nasopharyngeal carcinoma by up-regulating TGF-β1.