Donna Pincus, a clinical psychologist and director of the Child and Adolescent Fear and Anxiety Treatment Program at Boston University, said at least part of this fear may be ingrained in the human psyche.
Children may start with a fear of the dark, then get over it and develop a fear of monsters, and continue the cycle with more complex adult fears.
"[Studies] show that even cross-culturally, fears show this kind of progression," said Pincus.
Very young children are likely to have a detachment fear, or fear of the dark, said Pincus. Preschool-aged children fear animals, kids may fear monsters, and tweens or preteens begin to develop social fears and anxiety.
"You actually can notice that the natural progression of fears follows a line of cognitive development," she said.
Luckily, most children who are afraid of bees or the neighbor's Rottweiler grow out of it.
"They're not called a phobia unless it's outside the range of normal," said Pincus. "It can really change the course of a child's life in many ways."
Pincus once treated two brothers who developed a phobia of dogs; one who was bit by the dog and the other, who saw it happen.
She said the brother who watched had a notably more severe phobia, but "both of the kids were refusing to go outside." Apparently the thought of possibly running into a dog on the street or in a neighbor's yard had produced a phobia so severe that the brothers might as well have had agoraphobia.
Pincus estimated about 2 to 4 percent of children have a clinical level of fear that would warrant treatment.
In some very rare cases, the child complaining of a stomachache and who doesn't want to go to school may have a true school phobia, not just an excuse.
"Signs are they just start to be sick, they just might be sick or have headaches," said Hartstein.
Even if parents recognize the illness as a sign of fear, "oftentimes they are ignored and they're minimized, and kids are left to figure it out alone," said Hartstein.
But Hartstein says a true phobia can be worked out, and it could be an easier fear to overcome than many parents think.
Hartstein said many school phobias might be rooted in a more specific fear. Yet children may lack the sophistication to isolate why they are feeling afraid.
"Kids will generalize things much more," said Hartstein. "Kids may be afraid to go to school, because they may be afraid to go to the bathroom in the school."
"I had a girl who was acutely school refusing," said Hartstein. After much questioning, Hartstein realized her patient was actually fearing a bully in her class, but she had generalized the fear into a paralyzing physical reaction to the entire school.
"It went from being in the class, to being in the school, to just being on the block," said Hartstein. "She would stand there and hyperventilate."
"We had to do a lot of work on recognizing that it was a person, not just the class," she said.
In the end, Hartstein said the girl tried again with a different school. "Now she goes to school everyday," she said.
Believe it or not, there is a formal term for a vomiting phobia, called emetophobia.
Most people of try to avoid this unpleasant experience as much as possible but when it happens, they gargle and move on with their lives.