The two schools, a primary and a secondary, are in the same area.
The secondary school sent home students in one year group having found out about the positive case this morning, before contacting the HSE for advice.
The principal of the secondary school says the first year student had minimal contact with other pupils as they were only in school for three hours on Tuesday, having minimal contact with 28 other pupils.
The school in question has a total enrolment of 160.
When the school found out this morning, that the student had contracted the virus, other first year pupils were sent home.
Students in other classes are unaffected and the school is liaising with the HSE and other authorities.
According to Radio Kerry, the primary school in question sent home two classes after a pupil there also tested positive for the virus.
The primary school was contacted, but declined to comment on the situation.
This is the third day since schools reopened last week that a group of students have been sent home due to a confirmed case.
Yesterday, a school in Co Clare contacted students to inform them the school in the south of the country would be forced to close after a number of staff members were identified as close contacts of a confirmed case.
Earlier in the week, two Dublin primary schools sent a number of students home after a child tested positive for the virus in each school.
This comes after the HSE's comments earlier that they are very pleased with how schools have responded to recent cases of Covid-19.
Over one million students returned to class over the past week despite concerns from teachers, unions and parents.
HSE Chief Executive Paul Reid says each situation has been handled well.
"We have already experienced a number of confirmed cases in schools this week and I am pleased with the nature of the response.
"I would like to commend the principals and our public health teams, who act really very quickly and diligently, working with the schools.
"When a case has been identified in a school, public health teams are immediately in communication with the school," said Mr Reid.
