My 3 year old son threw up yellow yesterday morning, and ever since then he has been complaining of on and off headaches and fevers what could it be?

Viral syndrome. Acute onset of vomiting without associated cough or cold symtoms. Intermitttent headaches and fever treated "without a response" or "feeling comfortable" would be suggestive of a more serious illness. Persistent vomiting inspite of a trial of nothing by mouth stomach rest is also grounds for checking sooner than later. Small sips given over time with intro. To starches may be tolertated. Monitor!