Three-year-old Tyler Garnett was rushed to the Boultham Park Medical Practice in the hope that someone could tackle his illness.
But father Aaron Garnett, 29, says he was told his son could not be treated unless he could tell them the boy's NHS number – as Tyler wasn't a patient at the practice.
As a result, Mr Garnett – who is a registered patient – claims Tyler had to wait three days without treatment while he waited for the practice to open again in order to produce the card.
Now Mr Garnett, of Cotman Road near Skellingthorpe Road, in Lincoln, says he is looking for answers about what he claims happened to his son.
"For me, to send a three-year-old child away for that reason is not adequate," he said.
"We went to the doctors because he was not feeling very well.
"Then the doctors turned him away because I did not have his NHS number.
"They said they needed it to bring up the details of the patient."
He had been to the GP surgery on Friday, December 18 with Tyler, but when turned away had to wait until December 21 for another opportunity to have him treated.
Over the weekend, he rang the NHS Direct helpline, but says he was told that Tyler did not need to be taken to the accident and emergency department at Lincoln County Hospital.
Mr Garnett says that as a result, his son could barely eat for three days because of the discomfort he experienced when swallowing.
The surgery disputes Mr Garnett’s claims, but cannot go into any more detail because of patient confidentiality. The practice also said it wanted to reassure patients that, while it is helpful to provide their NHS number when registering at the surgery, it is not a requirement.