This study was designed to investigate the molecular mechanism and biological roles of long non‐coding RNA (lncRNA) brain‐derived neurotrophic factor antisense (BDNF‐AS) in colorectal cancer (CRC). The quantitative real‐time PCR (qRT‐PCR) and western blotting were performed to detect the expressions of lncRNA BDNF‐AS and glycogen synthase kinase‐3β (GSK‐3β) in human CRC tissues and cell lines. The cell proliferation, transwell migration, and invasion assays were carried out to evaluate the effect of lncRNA BDNF‐AS on the growth of CRC cells. RNA pull‐down and RNA immunoprecipitation (RIP) assays were conducted to confirm the interaction between lncRNA BDNF‐AS and enhancer of Zeste Homologue 2 (EZH2). Chromatin immunoprecipitation (ChIP) assay was used to verify the enrichment of EZH2 and histone H3 lysine 27 trimethylation (H3K27me3) in the promoter region of GSK‐3β in CRC cells. LncRNA BDNF‐AS expression was significantly decreased, while GSK‐3β was highly expressed in human CRC tissues and cell lines. Moreover, lncRNA BDNF‐AS induced inhibition of proliferation, migration, and invasion of CRC cells via inhibiting GSK‐3β expression. Mechanistically, BDNF‐AS led to GSK‐3β promoter silencing in CRC cells through recruitment of EZH2. In conclusion, lncRNA BDNF‐AS functioned as an oncogene in CRC and shed new light on lncRNA‐directed therapeutics in CRC. Significance of the study LncRNA BDNF‐AS is recently reported to be remarkably downregulated in a variety of tumours and served as a tumour suppressor. However, the functions and underlying mechanism of lncRNA BDNF‐AS in CRC pathogenesis have not been reported yet. Our study is the first to demonstrate the effect of lncRNA BDNF‐AS in CRC and revealed that lncRNA BDNF‐AS expression is negatively correlated with the aggressive biological behaviour of CRC. Further investigation demonstrated that lncRNA BDNF‐AS functioned as a tumour suppressor in CRC progression by suppressing GSK‐3β expression through binding to EZH2 and H3K27me3 with the GSK‐3β promoter, shedding light on the diagnosis and therapy for CRC.