Long noncoding RNAs play an important role in the occurrence, invasion, as well as metastasis of various human cancers, including hepatocellular carcinoma. Long noncoding RNAs can affect the biological functions of hepatocellular carcinoma cells by regulating various genes; however, only a small fraction of molecular mechanisms of long noncoding RNAs have been elucidated. In the present study, lnc AC010973.1 (lnc-ATG9B-4) was first identified by microarray analysis from 8 patients with hepatocellular carcinoma and confirmed by quantitative PCR in 176 patients with hepatocellular carcinoma. We demonstrated that lnc-ATG9B-4 was tightly relative to the tumorous size, TNM stages, portal vein tumor thrombus (PVTT), the tumor capsule, metastasis, degree of differentiation, and poor prognosis of hepatocellular carcinoma according to long-term follow-up data. In hepatocellular carcinoma cells, overexpression of lnc-ATG9B-4 promoted proliferation, invasion, as well as migration, while inhibiting lnc-ATG9B-4 by siRNA significantly attenuated the proliferation, invasion, as well as migration. Interestingly, lnc-ATG9B-4 increased the expression of cyclin-dependent kinase 5 (CDK5), which was closely related to the development and chemotherapy sensitivity of hepatocellular carcinoma. In summary, our results revealed that lnc-ATG9B-4 suggests an unfavorable prognosis of hepatocellular carcinoma and facilitates the proliferation, invasion, as well as migration of hepatocellular carcinoma cells by upregulating CDK5. This research suggests that lnc-ATG9B-4 may be a new biomarker for predicting the prognosis of hepatocellular carcinoma; meanwhile, targeting lnc-ATG9B-4 might serve as a potential strategy for the treatment hepatocellular carcinoma. Impact statement In this study, we explored the expression profile of lncRNA in HCC tumor tissues and paracancerous tissues using microarray assays. Furthermore, a new lncRNA (lnc-ATG9B-4) was identified, which was about 3.5 times more expressed in tumor tissues than in paracancerous tissues. Through clinicopathological analysis, lnc-ATG9B-4 was determined to be related to the tumorous size, TNM stages, portal vein tumor thrombus (PVTT), the tumor capsule, metastasis, and the degree of differentiation. Lnc-ATG9B-4 promoted the proliferation, invasion, as well as migration of the HCC cells by upregulating the expression of CDK5. Here, we further exploited the molecular mechanisms of lnc-ATG9B-4 to screen new drug intervention targets for recurrence and metastasis of HCC.