Bidens pilosa is used as an ethnical medicine for bacterial infection or immune modulation in Asia, America and Africa. Here, we employed an IFN-γ promoter-driven luciferase reporter construct and T cells to characterize immunomodulatory compounds from this plant based on a bioactivity-guided isolation principle. We found that PHA, a positive control, caused a six-fold increase in IFN-γ promoter activity. In contrast, hot water crude extracts from Bidens pilosa and its butanol subfraction increased IFN-γ promoter activity to two- and six-fold, respectively. Finally, centaurein (EC50 = 75 μg/ml) and its aglycone, centaureidin (EC50 = 0.9 μg/ml), isolated from this butanol subfraction, augmented IFN-γ promoter activity by four-fold. Consistent with the role of centaurein or its aglycone in IFN-γ regulation, we showed that centaurein induced the activity of NFAT and NFκB enhancers, located within the IFN-γ promoter, in Jurkat cells. Overall, our results showed that centaurein regulated IFN-γ transcription, probably via NFAT and NFκB in T cells.