As a result, the agency is requiring students who may have come in contact with the students to take antibiotics for Pertussis --better known as whooping cough.
At least 200 fourth graders and bus riders on bus 223 are among the students susceptible to whooping cough.
Deborah Usinger's daughter is one of them. She says she knows all about whooping cough, because her daughter had it as an infant.
"It was a little scary," she said. "We didn't know at first that that's what she had."
Students were not allowed in school Monday unless their parents could show proof their child is on antibiotics to treat the illness.
"They called the prescription in and, actually, we had to wait 24 hours because they ran out of the antibiotics," Usinger said.
School officials say nine students were turned away Monday. Their parents are in the process of getting doctors appointments and the necessary prescriptions so they can return to classes.
Click here to read letter to fourth grade parents
Click here to read letter to kindergarden parents
School officials say further immunizations are not required.
But parent David Beck, who has a four-year-old son at Carrboro Elementary, says he wasn't thrilled about having to do it a second time since another whooping cough case was discovered at the school in September. However, the vaccine doesn't always prevent whooping cough and it doesn't last forever.
"The rumor is that a lot of people have been using a loose, exemption policy to get kids in school that haven't been vaccinated," Beck said. "And I think that's what we need transparency on from the school system."
Chapel Hill-Carrboro school officials could not immediately provide figures on exceptions at this school to the vaccination policy, but that should be available to parents.
Whooping cough is highly contagious from a sneeze or cough. It causes a constant, hacking cough that can leave children nearly breathless. It can be deadly in infants and the elderly.
While it's not 100 percent effective, experts say the DTaP vaccination is the best prevention.
Health officials say they can't prove or disprove a link between the outbreak in December and the current one.
"I don't think it's a coincidence," Usinger said. "I think, you know, certainly with something like whooping cough, I mean, it's - especially with older kids it might just look like a cold and just go undiagnosed." In last November, there were seven reported cases at Estes Hill Elementary which is also in Orange County.