This paper presents a novel fault tolerant control system for Hall Effect position sensors failure of permanent magnet brushless DC (BLDC) motor in a closed loop control scheme. The proposed system is capable to detect and identify the Hall Effect sensors breakdown based on sensors signals and Discrete Fourier Transform (DFT) analysis of the measured line voltages of motor. In this paper behavior of BLDC motor is studied for Hall Effect sensors breakdown through simulation model. BLDC motor simulation model were validated first by experimental data under no fault condition. Analyzing the simulation results of the various sensor breakdowns leads to develop an expert system for Hall Effect sensors failure diagnosis in BLDC motor. A simple method is presented to generate the commutation signal of faulty Hall Effect sensor to maintain the proper operation of BLDC motor after fault occurrence. The proposed fault tolerant control system does not need massive computational efforts and can be implemented as a subroutine in the main control program of the BLDC motor. The simulation results show correct performance of the proposed fault tolerant control system.