Three-phase synchronous motors are widely used in the industrial motor driven systems. Variable frequency drives (VFDs) which allow soft-start of motors produce PWM voltage. Numerical relays are used in the protection schemes of these high voltage motors. The location of current transformer (CT) is an important criterion in the protection circuit. Impact of harmonics and the location of current transformer in the motor starting circuit is analysed considering a case study. A suitable protection strategy recommended by IEEE for synchronous motor driven by VFD is presented.