A large genetic association on miRNA related genetic variations recently identified single nucleotide polymorphisms (SNPs) in Pyruvate dehydrogenase kinase1 (PDK1), to be associated with prostate cancer (PCa) risk. This gene is activated under hypoxic conditions and encodes for mitochondrial enzymes associated with metabolic pathways. Our genome wide association studies (GWAS) identified two SNPs,rs1530865 (G>C) and rs2357637 (C>A), in the 3’UTR of PDK1, which were predicted to alter miRNA binding to the PDK1 gene. We hypothesised that PDK1 is involved in PCa progression by regulating cellular metabolic pathways under normoxic and/or hypoxic conditions via miRNAs. Higher expression of PDK1 was observed in PCa cell lines under hypoxic versus normoxic conditions. Under normoxic conditions, knockdown of PDK1 did not affect proliferation of LNCaP and PC3 cells however, the rate of migration and invasion was decreased. Furthermore, suppression of PDK1 reduced aerobic glycolysis, glycolytic demand and glycolytic reserve in PCa cells indicating that aerobic glycolysis (conversion of glucose to lactate even in the presence of oxygen) may promote PCa tumorigenesis. Computational predictions revealed that PCa risk associated rs1530865 SNP was predicted to affect the binding site for miR-877-5p, miR-3125, miR-3916 and miR-3928-3p and rs2357637 for miR-889-3p and miR-2116-3p miRNAs. Reporter gene assays confirmed that miR-3125, miR-3916 and miR-2116-3p have a specific affinity for the rs1530865 SNP C-allele and rs2357637 SNP A allele respectively. In conclusion, our findings demonstrated strong evidence for the role of miRNAs in the regulation of PDK1 in PCa in an allele dependent manner, which in turn regulated PCa metabolism.