You don't say how old these cats are or whether or not they have been spayed and neutered. If they have not been, that is the first place to start. The male will have much less tendency to be aggressive once he is neutered.
If they have both been spayed/neutered, then my next thought is that the male is really enjoying entertaining himself by beating up on his sister. A couple of things come to mind here: First, the more you can wear out the male by playing with him, the less he will entertain himself by stalking his sister. I would definitely try something like a "kitty-tease". A kitty-tease is a fishing pole-type of toy with a little bit of cloth at the end of the string. When drawn along the floor, or any surface, the little bit of cloth moves amazingly like a bug and kitties go nuts chasing it. I would try to play with the male several times a day and really wear him out. I would also play with him with the kitty-tease any time you notice him stalking his sister. Distracting him from annoying her by playing with you could solve the problem. Another thing that I have found works with cats who love to "attack" is a small stuffed toy about half-size to slightly smaller than the cat. A soft stuffed dog toy works great. These cats love to "attack" the toy, bite and kick it. Your male kitty sounds like he needs an outlet for his energy and desire to roughhouse.
The other possibility that comes to mind is that sometimes it works well to add to the family another young cat who loves to roughhouse. The two wild ones often play hard and wear each other out and leave the more sedate and timid cat in peace. Of course, adding an additional cat isn't always a possibility.
Besides trying to wear out your rambunctious male, I would try to put your female in a safe, quiet area away from the male when you are not home to supervise. With time and maturity, your male will probably begin to mellow. Until then, I hope these suggestions help.
Dr. Humphries gave you some great advice. One other hint that can help is to put a collar with a bell on the male. That way the female can know better where he is and avoid him better.
It would be good to have a veterinary exam as well. Sometimes a medical problem such as a painful tooth can make a cat feel vulnerable and lead the other cat to pursue her more.
This could also be territorial aggression. You need to separate your cats until you can get help . THis is a quality of life issue for your female and it not fair for her to constantly be looking over her shoulder - that creates a great deal of stress and can even lead to illness/medical problems.
We have a DVD called "Helping Kitties Co-Exist" available on our website www.HelpingKitty.com. Many behaviorists will do telephone consults for cat problems - find one at CertifiedAnimalBehaviorist.com. But the more opportunities your male has to harass your female, the better he gets at it, the more frightened she becomes and the chance for the cats getting along well decreases. So you need to separate them and then get a plan together - either from our DVD or hiring a consultant to help you.