The Arabidopsis gene AVP1 encodes a vacuolar H+-translocating inorganic pyrophosphatase (EC3.6.1.1) that functions as an electronic proton pump in the vacuolar membrane and affects growth development and stress responses in plants. This study was conducted to evaluate the molecular properties of the A. thaliana vacuolar H+-pyrophosphatase (AVP1) gene in rice. Incorporation and expression of the transgene was confirmed by PCR and quantitative real-time PCR, respectively. Expression of the AVP1 gene in transgenic rice plants (TRP1 and TRP2) resulted in significantly enhanced tolerance to 100 mM NaCl under greenhouse conditions when compared to control wild-type (WT) rice plants. Augmented AVP1 expression in the transgenic rice plants also affected total biomass and improved ion homeostasis through increased accumulation of Na+ ions in whole tissues when compared to control WT rice plants under high salinity conditions. The Fv/Fm values of transgenic rice plants were higher than those of WT rice plants, even though the values decreased over time in both WT and transgenic (TRP1 to TRP8) rice plants. Furthermore, rice grain yield and biomass of the transgenic rice plants were at least 15% higher based on the culm and root weights and panicle and spikelet numbers when compared to those of the WT rice plants during the farming season in Korea. Thus, these results suggest that ectopic AVP1 expression conferred tolerance and stress resistance to genetically modified transgenic crop plants by improving cellular ion homeostasis against salt conditions, which enhanced the rice yield and biomass under natural conditions in paddy fields.