A novel fractional delay estimation based on the adaptive algorithm is proposed to estimate the loop fractional delay in order to solve the problem of loop delay in Digital Predistortion(DPD) system. The high accuracy of estimation guarantees the correct extraction of the digital predistortion’s parameters. The proposed algorithm can improve accuracy and robustness of the fractional delay estimation by multi-point average, which eliminates the effect of the estimation error. Simulation results demonstrate the proposed algorithm has higher accuracy and robustness than the state-of-the-art algorithms, in which the accuracy increases to 1.4% of one sampling time period. The proposed algorithm can adaptively update the fractional delay in the system, which is of significance in the hardware implementation.