If your board’s SOC has a general purpose timer (GPT) then you can often have it count cycles of a hardware clock and store the value every interrupt pulse from

If your board’s SOC has a general purpose timer (GPT) then you can often have it count cycles of a hardware clock and store the value every interrupt pulse from a GPIO. I designed a GPS disciplined oscillator like this where we had an ADC generate a tuning voltage for a 100 MHz OCXO (which was a reference clock for microwave converters) which we divided down to 10 kHz and fed into the GPT, along with the 1pps from a GPS module, and the control loop would try to adjust it until we got 10K clock cycles for every pulse. This kind of synchronisation gets very accurate over a few minutes. Even just triggering an GPT from an GPS PPS input counting cycles of an internal clock you could use a GPT to work out the error in the clock, and you only need to query it once a second.