5.5 mm kidney stone just removed thru medicine. Is it harmful to take protein powder for gym purpose after that. Will it create stone again?

Need to drink water. If it is the first time you had the kidney stone usually there is no need for further testing. Taking protein supplements may cause stones but more important is to drink plenty of water. Urine should look clear. Also need to lower salt intake. Check with your doctor for specific dietary restrictions.
No. Just drink plenty of water. Make sure your urine is always clear, never dark. Your physician may have specific recommendations based on the exact nature of the stone.