Phosphate (Pi) deficiency in soil is one of the limiting factors to a growing plant due to its slow diffusion and high fixation in the rhizosphere. Brassica rapa plants were grown hydroponically under replete (P+) and deplete (P-) conditions to examine the variations in the expression of Pi responsive genes using real-time quantitative PCR (qPCR). Nine candidate reference genes were selected from the NCBI database. TATA box and SAND were selected as the most suitable reference genes under Pi-replete and Pi-deplete conditions due to their high efficiency and quality. The selected reference genes were validated by analyzing the expression of 14 target Pi responsive genes. The expression analysis of B. rapa root samples under Pi deficiency revealed the variable expression of genes; Bro18-014187 (ALMT1), a gene that is involved in organic acid exudation (OA) in the root system to promote phosphorus use efficiency (PUE) in plants, showed the highest increased (7.6-fold) under Pi-stress. Meanwhile, the expression of genes Bro18-047862 (PAP12), Bro18-038689 (MATE), Bro18-038513 (MMDH1), Bro18-004703 (SUC2), and Bro18-025411 (SUC2) increased with 3.69-fold, 1.9-fold, 1.4-fold, 3.03-fold, and 1.8-fold, respectively. Decreased gene responses were seen in Bro18-009479 (CS4), Bro18-042204 (ALMT1), and Bro18-035630 (MATE), while five other genes Bro18-039999 (PAP12), Bro18-049018 (CS4), Bro18-006954 (ALMT1), Bro18-035465 (MMDH1) and Bro18-013770 (MMDH1) remain unchanged. The whole-genome triplication (WGT) event in B. rapa led to three copies of paralog genes and transcription analysis showed the robust variation in the expression patterns of these paralog genes. Genes involved in signaling, transport, extracellular Pi scavenging, physiological function, and metabolic pathways are among the most highly expressed genes. This research provides a general overview of Pi’s influence on plant growth processes as well as presents particular experimental data on B. rapa responses to Pi deficiency.