My 6 weeks baby has been vaccinated today and she is taking medicines for her cough.is it ok.

Yes: There is no increased risk of an adverse reaction if you get vaccinated while you have a mile illness and even a fever. The vaccines will be effective as well. One reason why sometimes vaccines are deferred if someone is sick is that the vaccines can sometimes cause a fever in the next day or two and then the doctor cannot be sure if the fever is from the shots or the original illness.