probably get your gait checked to make sure you are not trying to lift your feet the wrong way, apart from that i would say try ice them and also stretch the muscles while they are warm.
Are you using proper running shoes? Even then it would be best to get your gait checked in case you've got the wrong 'type' of shoes.
The shoe thing did occur to me, and doing some research today it looks like I'm wearing the wrong ones. I'm using Nike Lunar Glides at the moment which are listed for stability but I'm a big under-pronator so I guess I should be more on the neutral end of things.
Have just been to physio for peroneal pain - my problem was with running/walking technique. Over a number of years I've lengthened the peroneal tendons which has caused a weakness in them. Perhaps wearing the wrong shoe has cause this problem with you?
Only way to cure pain is rest, ibuprofen and possibly some ice/elevation if swollen.
Good luck with the couch to 5k program!
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