Treatment. The best treatment for whooping cough is prophylactic, which comes in the form of vaccinations and keeping healthy people away from people who have the disease. Antibiotics given to the patient in the early stages of whooping cough can make the symptoms less severe and can lower the risk of the bacteria being spread. People who live with or must come into contact with the sick person are also given antibiotics even if they’ve already had the whooping cough vaccination. The patient should be given plenty of fluids and the disease should run its course after about six weeks. The rule of thumb is two weeks with the cold-like symptoms, two weeks with whooping cough and two weeks of recovery.