Background: Gastric cancer (GC) is a leading cause of cancer-associated death worldwide. Its molecular mechanisms, especially concerning autophagy and various signaling pathways, are not fully understood. Fatty Acid Binding Protein 6 (FABP6) and RE1 Silencing Transcription Factor (REST) emerge as potential key players in this context. This study sought to analyze the functional relationship of FABP6 and REST concerning autophagy and their implications on the Akt/mTOR signaling pathway within GC cells. Methods: A comprehensive bioinformatics approach was used to identify key prognostic markers in GC. The effects of FABP6 and REST on autophagy along with Akt/mTOR signaling pathways were analyzed by techniques including Western blotting (WB), flow cytometry, Transwell assay, dual luciferase reporter assay, and others. Results: FABP6 was identified as overexpressed in GC, linked with poor prognosis. FABP6 silencing reduces GC cell proliferation, induces S- and G2-phase arrest, and downregulates cyclins CDK2 and CDK4. It also inhibited GC cell invasion/migration and autophagy, effects that were counteracted by MG132. When combined with PI3K inhibitor LY294002c, FABP6 knockdown showed synergistic anti-proliferative effects, modulating the Akt/mTOR pathway. Besides, the transcription factor REST has been shown to directly regulate FABP6 expression, affecting autophagy and the Akt/mTOR signaling pathway in a FABP6-dependent manner. Conclusions: REST positively regulates autophagy and negatively affects the Akt/mTOR signaling pathway in GC cells in a FABP6-dependent manner, providing valuable insights into regulatory networks involving FABP6 and REST.