Did this today, I did find it hard going - but persevered !!
My knees are now killing me & the thought of running again on Wednesday fills me with dread. I have had no physical problems up to now.
I do have flat feet, but my running shoes are designed for over-pronation.
Any advice please.
It could be the route you ran put extra strain on joints and muscles that haven't been used to all that hard work and are just protesting a bit. Icing them and something like ibuprofen gel or tablets might be helpful to ease the pain and reduce any inflammation. If you're in any doubt, a trip to the Doctors or a Sports Physio might be a good idea.
On a practical note though, are you trying to run too fast, a very common error, or are you possibly overstriding?
You might not think you are but the next time you go out (make sure your knees have recovered before you do!) really think about the length of your stride. Take short steps with your feet ideally landing in line with your body, not in front of it.
Don't land on your heel - that can be a major cause of knee pain! Try to land mid-foot. Try not to land too heavily, keep the landings as light as you can by not lifting your feet too far off the ground, just far enough to stop you tripping over them. 
And keep it slow and steady! However fast you start out, slow it down a little - you'll be surprised what a difference that can make.
Hope they get easier with some rest and that you can carry on before too long😊
Does your week have to be set. I run day 1 walk day 2 rest day 3 repeat.
Everything davelinks says! Please take some extra rest days! Don't run if your knees are killing you. If you rest them now, a few days and you should be fine. Just one other thing, when my knees started playing up (around week 3), I started doing knee exercises just to strengthen them (in addition to all the other advice). I still do them daily and they have helped incredibly. Take it easy and hope they settle down quickly 
I agree with knee exercises, lunges etc, these exercises can be found on the NHS Couch to 5K site here nhs.uk/Livewell/c25k/Pages/...
Listen to the lovely davelinks , and listen to your knees.. They are pests...many of us have had the twinges !
Try, to run slowly and lightly, pull back and concentrate on the way your foot lands. I know, it felt really hard trying to emulate Laura's advice of the foot moving in a round cycling motion.. but it works...used make me giggle when I was doing it... but I still think about that even now.
The strength and flex exercises linked to this programme, I found brilliant... did them on rest days..and as Dave says, it could be the route... is there anywhere a little less hard underfoot , that you may be able to run
I had serious doubts week 5 that I could complete the program and continue running. Knees were very painful, stopped running started RICE and doing strengthening/yoga exercises especially to loosen very tight right hip. I'm back on track now week 8 all going well, I have no doubt I can complete and continue, quite happy to have two days rest if my knees complain. Take the brilliant advice posted on here dont give up but get your knees checked if the pain persists, good luck
Physio suggested strength exercises for thighs to support knees .. 😊 Not instant but did work. There are rugby and football pitches near me.. boring but easier on all joints.
Please take the advice here and put in extra rest days. My knees hurt last week and so I missed one of my usual days and was fine a few days later and so could run again. Just take it steadily and slowly and you will make progress. This is a change for life not a quick fix- at least that is what I keep telling myself!
Yes I echo all the excellent advice already given here . Please take extra rest days if needs be.
It could be new runners niggles , but best take extra rest days rather than risking injury and a long lay off. It doesn't matter if the programme takes you longer than 9 weeks , and yes I agree with Lon70 , its a change for life, not a quick fix .
Hope you feel better soon. Baby steps .... xxx
Like the others have said, I had a dodgy knee when I started and doing exercises helped. I go to the gym and do single as well as double leg presses on the machine, but others have given you links to other exercises.
