For the past two weeks I've been experiencing throbbing headaches when I go on my daily running exercise. Any suggestions on how to make it stop, ?

Exercise induced HA. Sometimes headaches can be induced by exercise- increased heart rate, circulation, sunlight, etc. I would contact a dr. If this continues. You may want to consider wearing sunglasses when you run if you are running outside and keep well hydrated.
Migraine. In some migraine patients, exercise exacerbates the headaches, and in others, may provoke. Best you discuss with your doctor, but perhaps your best bet is prevention, and many prescription and otc agents can do the job with minimal if any adverse effects.
First off make sure. That this is not from something serious. See your doctor soon for a work up. If this is not from something serious, there are medications that you may be able to take before physical exertion that can help. Again, i would see somebody very soon for this.