A couple things come immediately to mind. One important thing to consider is how you respond to her verbal expressions of fear, and other feelings. The best way to respond to feelings is to acknowledge them. For example, when she shares about something she is afraid of, you can reply, "You're really scared about that." Typically she'll respond with more information, and you can further reflect what you hear as the reason for the fear. Example, "It sounds like you're considering some of the pros and cons of being sexually active, and that whole HIV/AIDS thing has you pretty scared." You could follow that up with an affirmation of her good decision making skills or a validation that that is a difficult decision. If she doesn't open up with prompting, you can say, "I wonder what scares you the most about that." The point is to listen rather than talk, and let her know you're available to her when she wants to talk.
The second thing that comes to my mind is helping her distinguish between healthy and unhealthy fear. The purpose of fear is to protect us, and help us move away from danger and toward safety. Often our subconscious mind is aware of dangers before we consciously recognize them. It's important to listen to fear and identify the source of fear. Your daughter may be becoming more aware of her own sexuality and/or sexual feelings about a peer. A red flag about the dangers of unprotected sex can be very helpful in considering whether or not she will act on her sexual feelings. The problem many people have is in shutting off their fear, and not using the gift of healthy fear.
If these two suggestions don't seem to fit, or you try them and they don't help, you could talk to her pediatrician to see if she is showing signs of an anxiety disorder that might require therapy and/or medications. If there's a family history of anxiety or depression, it would be especially worthwhile to look into.
Even if there is an anxiety disorder, though, learning to cope with feelings by identifying, expressing them, and accepting them is the key to managing them! Hope this helps - would love to hear back about how it goes.