Hina Patel, 37, had "full sexual intercourse" with the teenagers when she was working as a supply teacher at Birkdale High School for boys near Southport, Merseyside.
A court was told that she had met the boys for sex sessions at her home in nearby Hightown over several weeks between February 1 and March 18.
Birkdale headteacher Gary Loveridge said that he was "appalled" by Patel's behaviour, and that she has been suspended as soon as the allegations emerged earlier this year.
"I am appalled she used her position in such a way," the Daily Mail quoted Loveridge as saying.
"We are relieved we found out at such an early stage - but it just shows how you have to be very vigilant and your processes have to be robust," he said.
Patel pleaded guilty to two charges of abusing her position of trust by sexual misconduct at North Sefton Magistrates Court, she will be sentenced at Liverpool Crown Court next month.
Chairman of the bench Caroline Spencer bailed Patel on condition she did not contact the boys or any pupils from the school. (ANI)