The PIC has several onboard hardware timers you could use for this, but I think just counting passes through the main loop would be much simpler for this application.
If you really want to use a hardware timer for this, look at
this IFI whitepaper. A polled timer should be good enough for your purposes, so you'd setup the timer in your initialization, then you'd start it and pre-load the correct values when you saw a pulse. as long as the interrupt flag is 0, it hasn't timed out and you should ignore pulses.