Gastric cancer (GC) is one of the most commonly occurring malignancies worldwide, and metastasis is one of the key processes affecting the prognosis of GC. TMEM41A, which belongs to a group of transmembrane proteins that participate in signaling pathways and tumor development, is a 264‑amino acid protein encoded by a gene mapped to human chromosome The exact role of TMEM41A in GC has not been determined to date. In the present study, the expression of TMEM41A in 147 cases of GC was analyzed with immunohistohemistry and the prognoses of these patients were analyzed. It was revealed that TMEM41A was highly expressed in GC tissues, and may be associated with the progression of GC and poor prognosis. The expression of TMEM41A was observed to be correlated with lymph node metastasis, distant metastasis and advanced tumor, node and metastasis stages. Knockdown of TMEM41A in vitro and in vivo decreased the GC cell migration ability by regulating epithelial‑to‑mesenchymal transition and cell autophagy, via the upregulation of E‑cadherin and downregulating N‑cadherin expression in GC cells by reverse transcription‑quantitative polymerase chain reaction (PCR), semi‑PCR and western blotting. Furthermore, TMEM41A upregulation was associated with the upregulation of p62 and altered the conversion of light chain (LC)3‑1 into LC3‑2 by western blotting. Knockdown of TMEM41A was also observed to affect tumor metastasis in nude mice. Therefore, TMEM41A may be considered as a novel therapeutic target for the treatment of GC‑associated metastasis.