This paper studies the effects of eccentricities faults (EFs) on sensorless operation of Switched Reluctance motors (SRMs). EFs are among widespread faults in SRMs which make machine airgap uneven and consequently change SRM characteristics such as phase and mutual inductances. One of the most common methods for indirect rotor position estimation is to apply high frequency pulses to idle phases. As phase inductances vary, current pulses may face some alterations which endanger the proper function of sensorless algorithm. This means machine operation will be impaired or even may be unsustainable. In this paper, via Finite Element Analysis (FEA) machine characteristics is examined under EFs and it is evaluated how they affect SRMs' performance. Two modes for injecting high frequency pulses, namely negative slope of inductance and minimum inductance zone have been considered for current pulses. It is shown that although employed algorithm for pulse injection in minimum inductance is relatively more complicated but it is more fault tolerant than pulsing in negative slope. Using FEA and Matlab/Simulink models the main achievements of the paper are validated.