Forkhead box protein 3 (FOXP3) is associated with tumor progression and prognosis in various types of tumor cells. We have recently reported that FOXP3 inhibited proliferation of gastric cancer (GC) cells through activating the apoptotic signaling pathway. In this study, we found that over-expression of FOXP3 inhibited GC cell migration, invasion and proliferation. To further investigate the down-stream proteins regulated by FOXP3, the label-free quantitative proteomic approach was employed to analyze the gastric cells stably transfected with FOXP3-containing lentivirus or empty vector. A total of 3,978 proteins were identified and quantified, including 186 significantly changed proteins. Caveolin-1 (CAV1) was one of those changed proteins up-regulated in FOXP3-overexpressed gastric cells, moreover, it is one of the node proteins in the protein-protein interaction network and the key protein involved in focal adhesion pathway by bioinformatics analysis. As the main constituent of caveolae, caveolin-1 interacts directly with several signaling molecules and acts as a tumor suppressor in numerous carcinomas. Further biological experiments confirmed that FOXP3 directly binded to the promoter regions of CAV1 to positively regulated CAV1 transcription in GC cells. In summary, our study suggested that FOXP3 plays a tumor-suppressing role in GC via positively regulating CAV1 through transcriptional activation, and this FOXP3-CAV1 transcriptional regulation ais may play an important role in inhibiting invasion and metastasis of GC cells.