The paper presents a decision tree (DT) induced fuzzy rule-based intelligent differential relaying scheme for transmission lines including unified power flow controller (UPFC) and wind-farms. The conventional distance relaying scheme fails miserably in protecting transmission lines including flexible AC transmission systems controllers such as UPFC and further, the protection issues become more challenging when wind-farm is integrated. The proposed protection scheme extracts features from the instantaneous voltage and current signals from both ends of the transmission line using discrete Fourier transform based pre-processor and computes corresponding differential features. The differential features are used to build the fault classification tree using a data-mining algorithm known as DT. Further, the fuzzy membership functions are drawn using the DT thresholds and the corresponding fuzzy rule-base is developed for final relaying decision. The proposed technique has been extensively tested (in MATLAB environment) for single circuit and double circuit transmission lines including UPFC and wind-farms with wide variations in operating conditions. The test results indicate that the proposed DTinduced fuzzy rule-based relaying scheme is highly reliable and robust for protection of complex transmission line including UPFC and wind-farm. © The Institution of Engineering and Technology 2014.