The Digital Dual Mixer Time Difference (DDMTD) circuit (in a simplfied version here), allows you to measure with high precision the phase difference between two very high frequency clock signals.
Blue signal is the master clock one at frequency Fn.
Green signal is the same Fn but delayed by a certain phase Phi.
DMTD clock is F_dmdt = Fn * N / (N+1).
Generated beat signals (orange for the master clock and red for the slave) will have a frequency of F_beat = F_dmdt - F_n, that is F_beat = F_n / (N+1).
Choose N so that the beat frequency is low enough to be sampled at very high resolution and the exact Dt_beat between the 2 rising edges can be measured with high precision.
The phase difference between the master and the slave clock can be calculated as:
Phi = 2 * pi * Dt_beat * F_beat
This example uses F_n = 38.46 MHz and F_dmdt = 38.31 MHz having selected N = 255 (aproximated values)