And those in more deprived areas were 2.5 times as likely to have missed two weeks or more.
It comes as the majority of schools across Scotland prepare to re-open for the autumn term next week.
Several Covid infection prevention measures will stay the same as last year, but the self-isolation system has changed.
Education secretary Shirley-Anne Somerville said she was “acutely conscious” of the need to minimise disruption for children, and that under the new guidance fewer children will need to self-isolate.
From Monday, children under 18 will no longer need to self-isolate after contact with a positive Covid case, so long as they produce a negative PCR test.
Figures published by the Scottish Government reveal that half of school children living in the most deprived areas of Scotland were not in school because of self-isolation for at least half a day in the past academic year, compared to 39 per cent of those from the least deprived areas.
The figures are based only on the periods when schools were open.
Some 29 per cent of those in the most deprived areas missed at least one week of in-person schooling, compared to 17 per cent of those in the least deprived areas.
Ten per cent of more deprived children missed two weeks or more, compared to just 4 per cent for children from wealthier areas.
Ms Somerville said: “We have been acutely conscious of the need to reduce educational disruption for our children and young people, while maintaining a safe and supportive school environment for staff, children and young people.
"When schools returned on a phased basis at the start of this year, we ensured that vulnerable children were among the first to be able to return to in-person learning as soon as it was safe to do so.
“The recently revised approach to self-isolation policy for under-18 close contacts means that fewer young people will have to self-isolate and most will be asked to self-isolate for a much shorter period of time.”