Land plants can utilize nitrate (NO3-) or ammonium (NH4+) as preferably nitrogen (N) source, however high tissue NH4+ accumulation presents potential harmful effects for cell metabolism, such as growth stunting and occasionally leading to plant death. Rice plants (Oryza sativa japonica cv. Nipponbare) are ammonium tolerant that have developed several mechanisms to cope with high NH4+ concentrations in paddy soils. Despite the NH4+ tolerance in rice plants has been known for a long time the physiological mechanisms involved in this process are still partially understood. Aiming to investigate if rice NH4+ tolerance is related to shoot NH4+ exclusion mechanisms, 30-day-old rice plants previously grown in Hoagland and Arnon solution were deprived of N for 3 days. Then, these plants were exposed to 10 mM NO3- or 10 mM NH4+, as sole N source, by 24 h in greenhouse conditions. After 24 h, nitrate and ammonium root influx were quite similar, but xylem NO3- flux was 7.6 times higher than NH4+ flux to shoot in NO3-- and NH4+-supplied plants, respectively. The concentration of ammonium and nitrate in leaf tissues were alike, while in roots the ammonium content was 4-times higher than nitrate content in NH4+- and NO3--treated plants, respectively. Net CO2 assimilation, stomatal conductance and actual quantum efficiency of PSII did not change in both NH4+- and NO3--treated plants. In fact, these results demonstrate that rice plants are tolerant to high ammonium concentrations, as reported in the literature. In conclusion, this NH4+ tolerance is related to the high compartmentalization of this ion in roots, inside of vacuoles or apoplast, reducing the xylem flux to shoot and accumulating small amounts of NH4+ in leaf tissues. This low concentration of NH4+ in green leaves allowed a normal photosynthetic activity and cell metabolism. Moreover, it is also important to highlight other exclusion mechanisms, such as an efficient NH4+ assimilatory system, particularly glutamine synthase and glutamate synthetase (GS-GOGAT) cycle which could be involved with ammonium tolerance in rice plants. However, further investigations are needed to better understand the mechanisms related to green leaves ammonium exclusion in rice plants.