Apparatus and methods for phase synchronization of phase-locked loops (PLLs) are provided. In certain configurations, an RF communication system includes a PLL that generates one or more output clock signals and a phase synchronization circuit that synchronizes a phase of the PLL. The phase synchronization circuit includes a sampling circuit that generates samples by sampling the one or more output clock signals based on timing of a reference clock signal. Additionally, the phase synchronization circuit includes a phase difference calculation circuit that generates a phase difference signal based on the samples and a tracking digital phase signal representing the phase of the PLL. The phase synchronization circuit further includes a phase adjustment control circuit that provides a phase adjustment to the PLL based on the phase difference signal so as to synchronize the PLL.