My cat won't eat, needs medicine. Can I give it on an empty stomach?

It's best to get the medicine in him, especially if it is an antibiotic. If there is something your cat cannot resist, such as cheese, or yogurt, try giving it to him after you give the medicine. That way he will come to associate getting the pill with getting a treat. Yogurt is especially good if your cat is getting an antibiotic as it helps reestablish the gut flora that antibiotics remove. Just make sure the yogurt you give does not have any artificial sweeteners. Plain or vanilla is best.
Not eating is a serious matter in cats. They cannot go more than a few days without eating or they risk liver damage.
Try enticing your pet to eat with beef or chicken baby food that does not contain onion or garlic power as an ingredient. Onion and garlic causes anemia in dogs and cats. Warm it in the microwave for a few seconds. Stir it with your finger first to make sure there are no hot spots and that it isn't too hot. This makes it more aromatic and appealing to your pet. Wetting dry food or mixing wet food with low sodium chicken broth, also warmed, might entice your pet to eat. Some cats like to be petted while they eat, some want to be left alone. You'll know your cat's habits and be able to act accordingly.