Medicinal plants have been known to act as a harbor for endophytic fungi, owing to their being able to produce bioactive compounds similar to those of their host. Thymus is a member of the Lamiaceae family. It enjoys a long history of traditional and modern medicine as a disinfectant that possesses antimicrobial properties. The pharmaceutical properties of this plant can be attributed to its endophytes. In this research, 89 endophytic fungi of Thymus spp. were tested and examined to investigate their biocontrol effects against the plant pathogenic fungus Botrytis cinerea, the plant pathogenic bacteria Xanthomonas arboricola pv. juglandis and Streptomyces scabies and human pathogens Escherichia coli ATTCC 25922 and Staphylococcus aureus ATCC 33591. Thereafter, to control fungal and bacterial pathogens, the extracellular metabolites of the endophytic fungi were extracted and used in seven different concentrations. The effect of endophytic fungi on the growth of B. cinerea suggested that the M24 isolate (Fusarium subglutinans) was the one with the greatest percentage of inhibition. Out of the 89 isolates tested against bacteria, only one isolate affected X. arboricola, three of them affected E. coli, and eight isolates showed biocontrol effect on bacterium S. aureus. In the case of S. scabies, all Fusarium isolates prevented its growth. Among other isolates, only M32 and M33, which belong to mycelia sterilia, affected the growth of this bacterium. Endophytic extracellular metabolites had great potential to control plant pathogens as well.