This is not a straight yes or no question as the answer is highly dependant upon first, the level of instability of the muscles that cross the ankle and second, the type and or construction of the AFO.  As a general rule, if the reason you are wearing the AFO is primarily an ankle instability issue, then in most cases you can run and be very active in the AFO just as many professional athletes wear knee braces during play.

With that being said, there are varying materials that these braces are made of and some are more designed for strenuous activity than others.  You should always ensure that you communicate to your doctor that you wish to run or do other activities in your AFO so that information can be taken into account with the construction and design of your particular device.