The aqueous extract of Eleusine aegyptiaca L. displays neuraminidase inhibitory value of 1.014μm. Neuraminidase inhibitors were isolated from aqueous extract of Eleusine aegyptiaca L. viz (-2-(2,4- dihydroxy phenyl)-5-hydroxy-8H-pyrano[3,2-g]chromen-4-one (1), 5-Hydroxy-2-(3-hydroxy-phenyl)-6- isopropenyl-chromen-4-one (2) and aesculetin (3). An ionization technique in mass spectrometry called Direct Analysis in Real Time Mass Spectrometry combined with a Direct Binding Assay was used to characterize the neuraminidase inhibitors. Minimum free-energy modeling analysis revealed the compounds (1, 2 and 3) forms an axis with inter-phenolic ring distances of 1.7 A, 1.3 A and 1.1 A respectively. Solvent Accessible Surface Area of compound 1 shows the 3D binding region of neuraminidase. Molecular docking was performed to analyze the binding between neuraminidase and compound 1.