Hurtful pain is a tolerable level of muscle soreness that develops after increases in training, especially downhill running and interval training. All athletes who add a new, vigorous regimen to their training will experience delayed-onset muscle soreness (DOMS) a day or two after the new exercise. This type of pain can be treated successfully with just a few days' use of ibuprofen (400 to 600 milligrams, two or three times a day).
Gentle exercise can help loosen up the sore muscles. I recommend substituting stretching and low- to non-impact cross-training sports when a new running regimen has led to DOMS. Though you can run with sore muscles if you want, you should start each run with a warmup, then do some light stretching and proceed cautiously.
Avoid fast or downhill running until the soreness is gone. You can continue to gradually increase your training, but monitor your soreness after each hard workout and, for several weeks, incorporate cross-training when necessary.
The second type of pain is harmful pain. This means a strong, throbbing pain around an injury site, possibly accompanied by swelling, warmth, and redness. With this type of pain, exercise becomes uncomfortable and will likely aggravate the injury. To help treat the redness, swelling, warmth, and pain, I recommend taking ibuprofen (400 to 600 milligrams per dose, two or three times a day) for up to two weeks if needed.
Naturally, you should see your doctor if the pain is severe. Also, take off at least five days from running, and cross-train instead. Then, to restart your running, try 2 to 3 miles of easy running mixed with walking, and pay attention to any worsening of the symptoms. If this workout doesn't irritate the injury, you're safe to continue running, but only two or three times a week for several weeks.
Keep in mind that ibuprofen can cause side effects such as stomach upset, so it's best to take this medication with meals. Also, since some research suggests that anti-inflammatories like ibuprofen can actually slow tissue healing and adaptation, don't treat DOMS with ibuprofen for an extended period while you're increasing your training volume or intensity.