More than likely, your seat (called a saddle in cycling speak) is too high or low. Literally, a centimeter or less up or down can make all the difference in the world.
Where It Hurts Determines How You Adjust Your Seat
If you hurt in the back of the knee, your seat is too high. If your knees hurt on the front of the knee or the outside of the knee, your seat is too low, and you need to raise it.
When making adjustments to your seat, you need to do so a tiny bit at a time. Raise or lower it only a centimeter (quarter of an inch) at a time and ride some more. If your knee still hurts, do it again. It may take several sessions to get it just right. Or, better still, take your bicycle into a bike shop and have them fit you to your bike. Then, once you find the sweet spot, mark your seat height with a marker on the stem so if for some reason your seat gets loose, you can put it back.
How To Determine Bicycle Saddle Height
The height of your saddle is based on your inseam length. (Your inseam length is from the base of your crotch to the floor.) Your saddle is correctly positioned when you are sitting squarely on the saddle with your down leg fully extended and the heal of your shoe touching the pedal comfortably. (You are not going to pedal with your heal, but that is how you make the measurement.) Make sure when you do this, you have someone else holding your bike, or have your bicycle securely on a trainer.
Once the height of the saddle is correct, you can change the front and back positioning on the bicycle. To do this, again have someone holding your bike from the back. Put both feet into the pedals with the ball of the foot over the pedal axle and move the pedals to a level position. Drop a plum line from the center of the knee (behind the knee cap). If the string does not fall directly in line with the pedal axle, move the saddle forward or backward until it does.
Let The Pros Do it
Honestly, it is much easier to have a bike shop help you with this than to do it yourself. Many will help you adjust your bike even if you didn't buy it there, and most do it for free.
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