A system and method for controlling polarization in a fiber amplifier is disclosed. A polarization dither waveform is applied to a polarization controller so that dithering does not trigger PI-HOMI (Polarization-Induced High Order Mode Instability). The dither waveform may have a period that is much less than the thermal diffusion time across the fiber amplifier core. The dither waveform may also have a slew rate (defined in degrees/second on the Poincaré sphere) that is much slower than the thermal diffusion time across the fiber amplifier core.
