A phase locked loop (PLL) system for mitigating non-linear phase errors stemming from time-variant integral non-linearity of the LO feedback phase quantizer (TDC) is disclosed. The system includes a phase modulation circuit which is configured to generate a plurality of phase shifts for a reference signal; select a phase shift of the plurality of phase shifts and introduce the selected phase shift into the reference signal, thereby modulating the phase difference between the feedback and the reference signal. Alternatively, the above phase modulation can be applied on the feedback signal path, attaining equivalent results. TDC is configured to quantize the phase of the LO feedback signal relative to the shifted reference signal to generate a phase detection signal, effectively modulating the non-linearity contributed error away from the LO center frequency. The phase detection signal is then digitally compensated for the intentional fractional frequency shift to allow the PLL to generate LO signal the desired frequency.