[Harmony♥]

It's most likely you'll go into the examination room alone, just you and your doctor. I don't think they let anyone else into the room except the two of you, unless you ask for special permission. But, just in case, tell your mom that you'd feel more comfortable if she'd wait in the waiting area while you go through the examination, or whatever it is your going to the doctor for.
It's true that your doctor will end up asking if your sexually active, and due to paitent-doctor confidentiality, you can tell them to please not inform your mother, and they have to keep that a secret, even if your mother asks. If not, the doctor is going against their hypcratic oath they took when they became a doctor and got end up losing their license for it.
No worries. Take our advice and your mother shouldn't know.
Are you going to the doctor to get some form of birth control? If not, since your sexually active, you can visit the Planned Parenthood's to get birth control without your parents knowing. It's best to get on it now to reduce the chances of an unwanted pregnancy.