In the current study, five fungal endophytes (WR-1, WR-2, WR-3, WR-4, WS-6) were isolated from the roots and stem of Withania somnifera (L.) Dunal, and tested fungal culture filtrates (FCF) against the brain tumour (glioblastoma) cell line (U-87). All FCFs showed anti-tumour activity with an IC50 value of 3.5, 6.0, 3.2, 6.0, and 0.95 µg/mL, respectively. HPLC fractionation of WS-6 showed the presence of 11 compounds (A1–A11), all with good anti-tumour activities (IC 50 3.5, 5.0, 5.0, 3.6, 2.5, 1.7, 2.3, 2.7, 0.9, 1.8 and 0.4 µg/mL, respectively). We report for the first time, the anti-tumour activity of 1-Docosene, Phenol, 2,4-bis(1,1-dimethylethyl), 1,2-Benzenedicarboxylic acid, diisooctyl ester, Hexadecane, 1,1-bis(dodecyloxy)-, Benzene, 1,1'-(2-methyl-2-(phenylthio)cyclopropylidene) bis-, Naphthalene, 1,2-dihydro-1-phenyl- (A1–A6), identified by GC-MS. The rest (A7–A11) had earlier reports of anticancer activities on cell lines other than U-87. We conclude that endophytic WS-6 (Aspergillus fumigatus) produces antitumor compounds that might be helpful in future drug development against brain tumours, especially glioblastoma.