The transcription factor forkhead box protein M1 (FoxM1) and tyrosine kinase receptor Her-2, aberrantly expressing in various kinds of human malignancies, are closely related to the development of cancer. However, the correlation of them is still little explored, especially in gastric cancer. In current study, we examined FoxM1 and Her-2 levels in gastric cancers, and the clinical significance and association of them were further explored. As a result, FoxM1 and Her-2 expression were significantly higher in gastric cancer compared with para-cancer tissues and gastric cell lines (P < 0.01), while a positive association was found between the two genes at both RNA and protein levels (P = 0.007, P = 0.025). No significant association was observed between FoxM1 expression and clinic-pathological parameters (P > 0.1), whereas the positive frequency of Her-2 correlated with TNM stage significantly (P = 0.045). In addition, multivariate analysis showed Her-2 was not a prognostic predictor in gastric cancer (P = 0.625), while FoxM1 was independently associated with prognosis (P = 0.001), which especially affected the survival in patients with advanced stage (P < 0.01). These results suggest that FoxM1 and Her-2 are important diagnostic markers for gastric cancer, and FoxM1 is a favorable prognostic indicator in gastric cancer. FoxM1 may be a potential cellular target for therapeutic intervention, especially in Her2-targeted therapy-resistant cancers.