SUMMARY Iron (Fe) is an essential micronutrient for both plants and animals. Fe‐limitation significantly reduces crop yield and adversely impacts on human nutrition. Owing to limited bioavailability of Fe in soil, plants have adapted different strategies that not only regulate Fe‐uptake and homeostasis but also bring modifications in root system architecture to enhance survival. Understanding the molecular mechanism underlying the root growth responses will have critical implications for plant breeding. Fe‐uptake is regulated by a cascade of basic helix–loop–helix (bHLH) transcription factors (TFs) in plants. In this study, we report that HY5 (Elongated Hypocotyl 5), a member of the basic leucine zipper (bZIP) family of TFs, plays an important role in the Fe‐deficiency signaling pathway in Arabidopsis thaliana. The hy5 mutant failed to mount optimum Fe‐deficiency responses, and displayed root growth defects under Fe‐limitation. Our analysis revealed that the induction of the genes involved in Fe‐uptake pathway (FIT‐FER‐LIKE IRON DEFICIENCY‐INDUCED TRANSCRIPTION FACTOR, FRO2‐FERRIC REDUCTION OXIDASE 2 and IRT1‐IRON‐REGULATED TRANSPORTER1) is reduced in the hy5 mutant as compared with the wild‐type plants under Fe‐deficiency. Moreover, we also found that the expression of coumarin biosynthesis genes is affected in the hy5 mutant under Fe‐deficiency. Our results also showed that HY5 negatively regulates BRUTUS (BTS) and POPEYE (PYE). Chromatin immunoprecipitation followed by quantitative polymerase chain reaction revealed direct binding of HY5 to the promoters of BTS, FRO2 and PYE. Altogether, our results showed that HY5 plays an important role in the regulation of Fe‐deficiency responses in Arabidopsis. Significance Statement The WHO considers iron‐deficiency anemia the most prevalent nutritional deficiency, affecting ~30% of the world's population. The majority of people obtain iron primarily from plants. Despite significant progress in understanding how plants acquire iron from the rhizosphere and transport it within plants, we still lack the complete understanding of how plants sense and respond to iron limitation. Here, we identify a novel role of HY5 (Elongated Hypocotyl 5), a member of the basic leucine zipper (bZIP) transcription factors family under Fe‐limitation conditions. We provide novel evidence that HY5 regulation of BTS (an iron‐binding E3 ligase) is critical for the Fe‐deficiency responses in Arabidopsis. This study improves our knowledge about plant response to Fe‐deficiency as well as adds a new role in the repertoire of HY5‐mediated pathways.