I have no experience whatsoever with yoga or being flexible but here are my 2ct.
If your pain comes from your muscles (in the back of your legs for example when trying to touch your toes) stretching every day will help, but it will take a lot of time if you are not used to it.
If the pain is in your joints (or your knees as you say) it might be something different and I would suggest seeing a doctor about it. This is not really normal as far as I know.
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