The paper presents an intelligent relaying scheme for transmission line in presence of UPFC. Transmission line distance relaying in presence of FACTs devices like UPFC has been a very challenging task. A new differential feature based approach using DFT based pre-processor and Decision tree (DT) is presented here for protection of transmission lines containing UPFC. A case study considering a 500-kV Transmission line of length 400-k.m(both single circuit and double circuit) is taken for simulation purpose in MATLAB environment and the results obtained show feasibility of the proposed relaying scheme. © 2013 IEEE.