This research studied the influence of phytochemical compounds on the germination time of pigeon pea (Cajanus cajan (L.) Huth). Over the 72 hours germination period, the contents of total and most individual free amino acids, particularly histidine, showed substantial increases. The content of γ-aminobutyric acid (GABA) was also greatly increased, from 0.24 µg/g to 2.7 µg/g, representing a nearly ninefold increase. The total phenolic content (TPC) and total flavonoid content (TFC) were positively related with germination time, with TPC highest at 62.49 mg GAE/100 g DW at 72 h, and TFC increased from 18.87 mg RE/100 g DW to 30.05 mg RE/100g.DW at 72 hours. The contents of individual phenolic acids and flavonoids, such as, protocatechuic acid, p-coumaric acid, ferulic acid and rutin, experienced noticeable increases. However, vanillic and catechin were only detectable at 72 hours, respectively. Antioxidant capacity measured by DPPH and FRAP assays increased from 102.30 to 128.95 mgTE/100g DW and 694.13 to 836.93 mg FeSO4/100g DW mmol/g, respectively, and therefore highlighting the enhanced antioxidant potential of germinated pigeon pea. The results from Fourier-transform infrared spectroscopy (FTIR) supported these findings. The study emphasizes the potential of germination to enhance the phytochemical compounds of pigeon pea seeds.