It’s called a “stress” fracture, because it results from repeated excess stress. The solution is to put less stress on the foot.
Are you running BARE foot? or in minimalist shoes? This type of injury is most common while running in shoes, especially minimalist shoes (due to muffled or blocked feedback to the soles, that would make putting excess stress on your foot very uncomfortable – way before a stress fracture).
Are you trying to run up on your fore-foot? Do NOT do run up on the toes or fore-foot! Instead let your entire foot land. If you feel your heel pounding, bend your knees more. If your heel isn’t touching at all, relax your calves more.
Finally, and perhaps most important; LISTEN to your BARE soles. They are sensory organs (unless we effectively blindfold them). Our bare soles are extra sensitive to help discourage us from putting too much stress on our feet, or any other part of our body.
If you can’t run gently for a short distance on rough gravel, then you’re not ready to run barefoot (or especially not in footwear!) any distance on any surface. Focus on learning technique first – after that, running longer, faster, and more frequently will come easily.