Boron (B) is an essential element for plants, and B deficiency is a worldwide agricultural problem. In B-deficient areas, B is often supplied as fertilizer, but excess B can be toxic to both plants and animals. Generation of B deficiency-tolerant plants could reduce B fertilizer use. Improved fertility under B-limiting conditions in Arabidopsis thaliana by overexpression of BOR1, a B transporter, has been reported, but the root growth was not improved by the BOR1 overexpression. In this study, we report that enhanced expression of NIP5;1, a boric acid channel for efficient B uptake, resulted in improved root elongation under B-limiting conditions in A. thaliana. An NIP5;1 activation tag line, which has a T-DNA insertion with enhancer sequences near the NIP5;1 gene, showed improved root elongation under B limitation. We generated a construct which mimics the tag line: the cauliflower mosaic virus 35S RNA promoter was inserted at 1,357 bp upstream of the NIP5;1 transcription initiation site. Introduction of this construct into the nip5;1-1 mutant and the BOR1 overexpresser resulted in enhanced expression of NIP5;1 and improved root elongation under low B supply. Furthermore, one of the transgenic lines exhibited improved fertility and short-term B uptake. Our results demonstrate successful improvement of B deficiency tolerance and the potential of enhancing expression of a mineral nutrient channel gene to improve growth under nutrient-limiting conditions.