Wild soybean (Glycine soja) is a leguminous species known for its ability to thrive in challenging and barren environments. It has been reported that the nitrate transporters (NRTs) play critical roles for plants to survive in the nutrient-poor soils. However, the molecular mechanisms of GsNRTs in governing nitrogen (N) uptake remain largely elusive. In the present study, we identified a NRT2.4-like protein (GsNRT2.4a) as an interactor of GsSnRK1.1 kinase. Our biophysical and physiological analyses indicate that GsNRT2.4a functions as an active NRT, and GsSnRK1.1 kinase phosphorylates the Ser518 residue at the carboxyl region of GsNRT2.4a. Under N starvation conditions, the double mutant nrt2.1/nrt2.2 (2nrtm) and the quadruple mutant nrt2.1/nrt2.2/kin10/kin11 (2kinm/2nrtm) exhibited compromised growth of Arabidopsis. However, introduction of GsNRT2.4a or GsSnRK1.1/GsNRT2.4a genes into the mutants rescued their defective growth to different extent. Furthermore, we determined that GsSnRK1.1 plays a pivotal role in modulating GsNRT2.4a activity in planta by phosphorylating GsNRT2.4a at the Ser518 site, thereby collaboratively modulating plant growth under N starvation. Our findings suggest that GsNRT2.4a is essential for optimising nitrate uptake in plants, and it also elucidates a novel regulatory mechanism of GsSnRK1.1-GsNRT2.4a module for potential enhancement of nitrogen use efficiency (NUE) in plants.