In my experience, pulsating of the brakes, especially if it is felt in the lever or foot pedal, is a result of warped discs.
This is particularly common on vented discs when they get really hot and the brakes are still applied quite hard when at a standstill.
I learnt a long time ago to release the brakes once I've come to a stop and then only apply them enough to hold the bike if on a hill.
I'm afraid it may mean disk replacement.