Distorted environment and human lifestyle require novel drugs in the different diseases; therefore, the present study was undertaken with fungal endophytes from Aloe vera. Total of sixteen fungal endophytes was isolated from the fifty root samples of Aloe vera collected from the different locations of Shrirampur, Ahmednagar district, India. All sixteen fungal endophytes were belonging to Fusarium oxysporum (20%), Nigrospora species (33%), Alternaria alternata (8%), Aspergillus species (50%), and Penicillium species (60%). The endophytic Penicillium species found to be a core group; therefore, the same fungus was grown in potato dextrose broth for the production of bioactive compounds and extracted with methanol solvent by solvent extraction method. The wet biomass of Penicillium species was recorded as 1.06 g/200ml and dried biomass recorded as 0.4 g/200ml of potato dextrose broth and 2.30 g/200ml of the crude extract were obtained. Further, six fractions were purified by the column chromatography and different bioactive compounds with Rf values such as alkaloids [0.32], flavonoids [0.43], flavonoids [0.43], terpenoids [0.16], and polar basic compounds [0.78] were purified from these six fractions under the influence of different solvent systems. FTIR analysis revealed different functional groups such as amide, alkanes, alkenes, alcohol and phenols, alkyl halide, ether, amines, and nitrile.