Make sure you are using proper form. My knees used to hurt until i worked on my form. Keep these elements in mind.
1. Weight should be on your heels, never on the balls of your feet, if your rock forward that puts strain on your knees. For this reason either squat barefoot, in socks, or in flat soled shoes like chuck taylors. Normal training shoes will encourage the rocking forward.
2. Start the movement by pushing your hips back. This reinforces #1. You should squat like you are sitting back in a chair. This puts the strain on glutes, hams, and then quads, not knees.
If this is hard to pick up start doing boxsquats. Take a regular bench and move it into the squatrack. When you squat, sit down on the bench like you normally would, pause for a breath, then look up, flex your glutes, hams, then quads and move your hips forward to come up.
Practice this with lightweight first. You should feel less and less pressure on your knees as you get better at it.
Good luck.