Boron (B) uptake in plants implies a passive diffusion through membranes under optimal conditions. Under deficiency or toxicity, the participation of two distinct protein families (the aquaporin family Major intrinsic proteins (MIPs) and the Boron transporter family BOR) is required to minimize detrimental effects caused by B stress that ends up inhibiting growth and altering development. Legumes comprise important crops that offer major agronomic benefits including the capacity of establishing symbiosis with rhizobia fixing atmospheric N2 and for being important food protein sources. It is well proven their susceptibility to B stress leading to important yield penalties. However, little is known about the transport mechanisms responsible for B uptake and distribution in legumes, especially under deficiency. This work aimed to characterize novel legume B transporter involved in B uptake under deficiency. A Medicago truncatula homologous protein to the Arabidopsis AtNIP5;1 was identified. Further analyses revealed that this M. truncatula aquaporin expression was boron-regulated in roots and localized at the plasma membrane of root epidermal cells and in nodules, where B plays pivotal roles in symbiosis. Furthermore, a partial complementation of the nip5;1 Arabidopsis mutant phenotype under B deficiency supports a functional role of MtNIP5;1 as a B transporter in this legume model plant opening new insights into boron transport in legumes.