As part of the reopening of education, some students who need to take part in practical teaching are able to return.
Speaking at the coronavirus briefing in Edinburgh on Wednesday, Ms Freeman said the “very small proportion” of the total number of students will be able to request a PCR test to “offer extra reassurance to them and their fellow students”.
“I would strongly encourage anyone who is returning to campus and who is changing households as a result to request a test,” she said.
Information is available through the NHS Inform website and the Student Information Scotland website.
Ms Freeman also addressed the latest plan for a phased return of pupils in Scotland’s secondary schools, as announced yesterday by First Minister Nicola Sturgeon.
Part of the safety measures include the continued provision of lateral flow tests for all school staff and senior pupils in S4-S6.
The Health Secretary said the Scottish government is publishing data on Wednesday showing the results of the first two weeks when these tests were available.
More than 36,000 staff and 3,000 pupils were tested, and Ms Freeman said “very few were positive”. She added that all positive results were among school staff.
Meanwhile, Scotland has recorded 35 deaths from coronavirus and 543 positive tests in the past 24 hours, Scottish Government figures show.
It brings the death toll under this measure – of people who first tested positive for the virus within the previous 28 days – to 7,371.
The latest statistics show 203,155 people have tested positive in Scotland, up from 203,012 the previous day.
The daily test positivity rate is 2.6%, down from 4.4%.
Of the new cases, 150 are in Greater Glasgow and Clyde, 77 in Lothian and 102 in Lanarkshire.
There are 750 people in hospital confirmed to have the virus, down 34 in 24 hours, and 69 patients are in intensive care, down two.
A total of 1,661,879 people have received their first dose of a coronavirus vaccine as of Wednesday morning and 8,105 have received their second dose.