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The locus at 17q12 erb‐b2 receptor tyrosine kinase 2 (ERBB2) has been heavily amplificated and overexpressed in gastric cancer (GC), but it remains to be elucidated about the clinical significance of the co‐amplification and co‐overexpression of PGAP3 gene located around ERBB2 in GC. The profile of PGAP3 and ERBB2 in four GC cell lines and tissue microarrays containing 418 primary GC tissues was assessed to investigate the co‐overexpression and clinical significance of the co‐amplified genes, and to evaluate the impact of the co‐amplified genes on the malignancy of GC. Co‐amplification of PGAP3 and ERBB2 accompanied with co‐overexpression was observed in a haploid chromosome 17 of NCI‐N87 cells with double minutes (DMs). PGAP3 and ERBB2 were overexpressed and positively correlated in 418 GC patients. Co‐overexpression of the PGAP3 and ERBB2 was correlated with T stage, TNM stage, tumour size, intestinal histological type and poor survival proportion in 141 GC patients. In vitro, knockdown of the endogenous PGAP3 or ERBB2 decreased cell proliferation and invasion, increased G1 phase accumulation and induced apoptosis in NCI‐N87 cells. Furthermore, combined silencing of PGAP3 and ERBB2 showed an additive effect on resisting proliferation of NCI‐N87 cells compared with targeting ERBB2 or PGAP3 alone. Taken together, the co‐overexpression of PGAP3 and ERBB2 may be crucial due to its significant correlation with clinicopathological factors of GC. Haploid gain of PGAP3 co‐amplified with ERBB2 is sufficient to facilitate the malignancy and progression of GC cells in a synergistic way. [ABSTRACT FROM AUTHOR]