BLDC motors are one of the motor types rapidly gaining popularity. In recent years various researches have been done in the field of motor fault detection and fault tolerant control. However, in the case of rotor problems, especially rotor eccentricity tolerant control a few papers have been presented. Since in sensitive industries, continuous operation with good performance till the maintenance time is very important, operating in the desired condition in presence of this kind of fault is really advantageous. But conventional control methods in presence of eccentricity fault are inefficient. Because they generate phase currents with the same amplitudes and equality of currents and inequality of back-EMFs and phase inductance changes due to eccentricity, leads to intensive torque ripples. So, a new control strategy which can improve motor performance is desirable. In this paper an on-line control method based on Back-EMF estimation is proposed which can increase quality of operation by eliminating load torque pulsation considering rotor eccentricity.