Pain from running, perhaps — affected after covering run (5)
I believe the answer is:
Here is my best explanation:
'pain from running perhaps' is the definition.
'affected after covering run' is the subsidiary indication.
'affected' becomes 'camp' (I've seen this before).
'after covering' indicates putting letters inside.
'run' becomes 'r' (cricket abbreviation).
'camp' enclosing 'r' is 'cramp'.
(Other definitions for cramp that I've seen before include "Painful involuntary muscle contraction", "Painful muscular contraction", "Muscle pain", "Restrict", "hamper", "common among writers", "A muscular spasm", "Give too little space to", "Muscular pain" and "Painful muscle problem".)