Fenugreek is an herb that has the ability to resist multiple environmental insults, pests, diseases and many pathogens through the synthesis of substances allowing this plant protection, these substances are called phytochemical compounds or secondary metabolites. The aim of this study is to characterize these secondary metabolites in the extracts of fenugreek seeds grown in Algeria and compare the phytochemical profile and antioxidant activity of the aqueous extracts obtained by maceration and decoction. We carried out a “phytochemical screening” on both types of extracts in order to highlight the different classes of secondary metabolites and assaying total polyphenols by the method of Follin ciocaltchu, total alkaloids and tannins contained in these aqueous extracts and appreciate their antioxidant activity using the FRAP technique. A characterization of phytochemical molecules of the two types of Fenugreek extracts was done by chromatographic method with HPLC. Several phytochemical groups were identified in the extracts of fenugreek: tannins, saponins, flavonoids, terpenes and reducing nitrogen compounds. Chromatographic analysis of the samples show that 4 phytochemical molecules were identified in the aqueous maceration extract: kaempferol, genistein, vanillin and myrecitine and 3 molecules for the aqueous extract of decoction are: rutin, kaempferol and vanillin. The aqueous extract of decoction was characterized by the total polyphenols content (31.7 ± 0.031 mg GAE / 100 g of extract), total alkaloids (2.12 ± 0.015%) and tannins (9.75 ± 0.06%) that are higher than those obtained in the aqueous extract of maceration: total polyphenols (18.9 ± 0.12 mg GAE / 100g of extract), total alkaloids (1.71 ± 0.02%) and 8.69 ± 0.02% for the tannins. A non-significant difference was marked for antioxidant activity found in both types of extracts (56.90 ± 0.013 mg AAE / 100g decoction extract against 56.37 ± 0.24 mg AAE / 100g maceration extract). In the end we conclude that fenugreek may be a promising plant genetic resource responsible for an important biological activity, except its nutritional and therapeutic properties due to their phytochemical compounds.