The boy was one of almost 3,500 who were called back for testing two weeks ago after it was discovered the doctor - who had administered vaccinations to the children - had been affected by TB for over a year.
The infected child has been admitted to the Burlo Garofolo children's hospital in Trieste, the hospital said on Monday evening. The hospital added that his condition "was not worrying" and that he was not in the contagious stage of the disease.
Tests were carried out on 3,490 children aged under six following the doctor's diagnosis, a measure the hospital described at the time as "precautionary and preventative".
Each of the children only came into contact with the doctor for a few minutes while the vaccination was being carried out, while the time it takes for the disease to spread, according to international protocols, is at least eight hours.
However, children aged under six have a higher risk of infection, the health authority said.
The hospital did not share the age or identity of the infected child.
"The protocol we have adopted is effective and safe," Nicola Delli Quadri, director of the local health authority said on Monday evening. "It allowed us to discover this case, and we won't change this protocol.
"We are working closely with the families and we understand what they are going through."
Delli Quadri added that after carrying out tests on hundreds of children, this was the only child who had tested positive for the bacteria. The process of testing all the at risk children is expected to take around another two months.