If by croup you mean that seal sounding cough, my son gets that all the time. My daughter never had it so it is true that some kids are more prone to it than others. Originally I was told whenever you hear that seal sounding cough, you should expose the child to heavy steam for 10 minutes and then extreme cold for 10 minutes and repeating two more times and it will make the cough stop. During the winter, we'd turn the shower on hot and sit in there away from the water and then bundle him up real good and take him outside for the cold part. During the warmer months, we'd still do the shower steam, but we'd let him sit on the floor or on one of his little chairs in front of the open refrigerator with a blanket over him for the cold part. Each time we've followed this routine, it's worked great to eliminate the croup.
Recently though, we took our son to the doctor for a sinus and ear infection and mentioned that those problems started after another croup episode. Our pediatrician gave us a sample of Singular and told us to break it up into 4 mg size (he only had 10 mg samples) and give it to him at night before bed whenever we heard the seal sounding cough. We crushed it up real good and put it in a drink or some food and It has worked beautifully!! He sleeps soundly and breathes through his nose with no problem when we give him the Singular.
You might ask your doctor about the Singular to see if it's something that would work for your son. My son is 5 though so yours may still be too young for that. Otherwise, the steam/cold routine works, but I will admit it's a bit tiresome, especially since it seems to always happen late at night, at least for my son. Good luck!
Blessings,
N.