Boron is especially required for the growth of meristem and reproductive organs, but the molecular mechanisms underlying the preferential distribution of B to these developing tissues are poorly understood. Here, we show evidence that a member of nodulin 26-like intrinsic protein (NIP), OsNIP3;1, is involved in this preferential distribution in rice (Oryza sativa). OsNIP3;1 was highly expressed in the nodes and its expression was up-regulated by B deficiency, but down-regulated by high B. OsNIP3;1 was polarly localized at the xylem parenchyma cells of enlarged vascular bundles of nodes facing toward the xylem vessels. Furthermore, this protein was rapidly degraded within a few hours in response to high B. Knockout of this gene hardly affected the uptake and root-to-shoot translocation of B, but altered B distribution in different organs in the above-ground parts, decreased distribution of B to the new leaves, and increased distribution to the old leaves. These results indicate that OsNIP3;1 located in the nodes is involved in the preferential distribution of B to the developing tissues by unloading B from the xylem in rice and that it is regulated at both transcriptional and protein level in response to external B level.