Treatment for prostatitis usually begins with taking an antibiotic for several weeks. If you begin to feel better, you may have to take the medicine for 2 to 3 months.If you do not get better while taking antibiotics, more tests may be done.reatment for prostatitis usually begins with taking an antibiotic for several weeks. If you begin to feel better, you may have to take the medicine for 2 to 3 months. If you do not get better while taking antibiotics, more tests may be done.