It is unlikely that your vagina will hurt a few seconds when he penetrates you due to kidney stones .
It is normally an infection, or you are too dry. You may also now tense up waiting for it to hurt, and that can make it hurt.
My advice is to use a good lube, spend a good few minutes on foreplay including him putting a finger or two inside to make sure you are wet and the muscles are relaxed, guide his penis with your hand to make sure it goes straight in.
If it does not go away after this, speak to your doctor.