The goal of the work is to determine the bioactive pharmaceutical metabolites produced by the Fusarium oxysporum YP9B isolate. Ten new natural compounds were isolated from the ethyl acetate extract of the F. oxysporum YP9B strain. Their structures were elucidated by spectroscopic methods using 1D and 2D NMR, UV, FT-IR, and mass spectra (LC-QTOF MS and GC-FID/MS). Identified compounds were named as; (1-benzyl-2-methoxy-2-oxoethyl)-2-hydroxy-3-methylbutanoate (1), 2-oxo-8-azatricyclo[22.214.171.124(3,7)]-hexadeca-1(15),3(16),4,6,11,13-hexaen-10-one (2), 2,3-dihydroxypropanoic, hexadecanoic anhydride (3a), 2,3-dihydroxypropanoic (9Z)-octadecenoic anhydride (3b), 2,3-dihydroxy-propanoic (9Z,12Z)-octadecadienoic anhydride (3c), 2,3-dihydroxypropanoic (11Z)-octadecenoic anhydride (4a), 2,3-dihydroxypropanoic, (9E,12E)-octadecadienoic anhydride (4b), 3-hydroxy-1,2,6,10-tetramethylundecyl hexzadecanoate (5a), 3-hydroxy-1,2,6,10-tetramethylundecyl (9E)-octadecaenoate (5b), and 3-hydroxy-1,2,6,10-tetramethylundecyl octadecanoate (5c). Antimicrobial activities of the isolates obtained from the YP9B strain were determined. Cytotoxic and antiviral activities were tested for the isolates against VERO, MCF-7, PC-3, and A549. Compounds 5a-c, 1, and 3a-c showed bacteriostatic activity at low concentrations, and 4a-b and 2 were found to be bactericides. MIC and MBC values against Mycobacterium smegmatis for the compounds 5a-c and 1 were determined to be <0.5 mu g/mL and 0.46 mu g/mL, respectively. The experimental result showed that compounds 2, 5a-c and 1 have strong cytotoxic (7.51 +/- 1.38 and 19.13 +/- 0.68 (mu M) IC50) activity. The antiviral activity against HSV type-1 was determined to be 1.25 mu M for compounds 4a-c and 0.312 mu M for compound 1.