In this study, novel endophytic fungi producing cajaninstilbene acid (CSA) from pigeon pea [ Cajanus cajan (L.) Millsp.] were investigated and screened. CSA has prominent pharmacological activities. A total of 110 endophytic fungi isolates were grouped into 8 genera on the basis of morphological characteristics, and CSA-producing fungi were screened by liquid chromatography-tandem mass spectrometry (LC-MS/MS). According to ITS-rDNA sequences analysis, the CSA-producing fungi were identified as Fusarium solani (ERP-07), Fusarium oxysporum (ERP-10), and Fusarium proliferatum (ERP-13), respectively. The amount of CSA produced by the ERP-13 reached 504.8 ± 20.1 μg/L or 100.5 ± 9.4 μg/g dry weight of mycelium. In a DPPH radical-scavenging assay, when the concentration of fungal CSA was 500 μg/mL, inhibition percentage could reach 80%, which was almost the same as that of standard CSA. This study first reported the natural antioxidant CSA from endophytic fungi F. solani and F. proliferatum isolated from pigeon pea.