Eucommia ulmoides Oliver is a traditional medicinal plant of China, and it is one of the main sources of chlorogenic acid. Chlorogenic acid is an ester of caffeic acid, quinic acid, and a phenolic compound that has antibacterial, antifungal, antioxidant, and antitumor activities. The purpose of this study was to determine whether endophytic fungi isolated from Eucommia ulmoides Oliver had the same ability to produce chlorogenic acid. Primary screening was done by antibacterial and antifungal reactions, and the strain reselection was done with high-performance liquid chromatography (HPLC) to identify the fermentation products of the selected strains. Extracts of the leaf and cortex of Eucommia ulmoides Oliver were also deteted by HPLC, then positive results of HPLC were analyzed by GC-MS and LC-MS. In this study, 29 strains were isolated from Eucommia ulmoides Oliver. Most of them had antibacterial activity, and a few of them had antifungal activity. One ingredient of the B5 extract had a retention time identical to that of authentic chlorogenic acid. With GC-MS, other ingredients, isocoumarin and p-chlorocinnamide, were found. With LC-MS, chlorogenic acid and geniposide related to Eucommia ulmoides Oliver were found. The strain B5 was identified as Sordariomycete sp. Thus, endophytic fungi may produce the bioactive compound chlorogenic acid, as their host plant does, and could be used for the production of chlorogenic acid by fermentation in the future.