More than 1,000 pupils were excluded from Glasgow secondary and primary schools last year.
At Holyrood Secondary School 88 children were told to stay at home after incidents including fighting and substance misuse.
Rosshall Academy had the second highest exclusion rate, with 70 pupils suspended for offences such as fire-raising and assault with weapons.
Glasgow City Council said exclusion was only used as a measure of last resort.
A Freedom of Information request revealed secondary schools across the city suspended 834 pupils last year while there were 310 exclusions from primaries.
Aultmore Park Primary ordered 21 children to stay away from class - the most in Glasgow for a primary - for reasons such as substance misuse, spitting and physical attacks on staff.
The charity Includem, which works to reduce exclusions in schools, believed that excluding children was not always the best solution.
Chief executive Martin Dorchester said: "We recognise there may be instances where exclusion is necessary and appropriate but this in isolation won't change behaviour in the long term.
"In Glasgow we work in partnership with the city council and schools to identify those young people who are likely to be excluded.
"The aim is both to prevent exclusion and to close the attainment gap by engaging them positively in school.
"Early intervention and preventative services are vital to tackle the root causes of problems before they escalate to the level where exclusion becomes the only option left for schools."
The latest statistics were uncovered after a Freedom of Information request to Glasgow City Council.
It was found that Hillhead High School had the third highest exclusion rate, with 57, followed by Bannerman High School at 54.
At one school, in the north of the city, at least one pupil was suspended for making a threat of sexual violence against another student.
Glasgow's Gaelic School temporarily excluded students for attacking their peers, while at Notre Dame all-girls high school, pupils were taken out of class for incidents such as slander and libel against staff, verbal abuse of staff and malicious communications.
Scotland's largest teachers union, the Educational Institute for Scotland (EIS), said that discipline was a major issue for teachers, parents and pupils.
An EIS spokeswoman said: "Whilst the majority of pupils in our schools are normally well behaved and eager to learn, there is a persistent minority of pupils who often fail to behave to an appropriate standard in the classroom.
"It is essential that in all schools effective strategies are in place to support class teachers in dealing with pupil indiscipline."
A Glasgow City Council spokeswoman said: "Since 2006, exclusions across the city have reduced by 74% - if children are not in school they are not learning and our schools work very hard to find alternative ways in which to meet the individual needs of our young people.
"Excluding a child or young person is always the last resort and we have developed a range of nurturing initiatives - including our very successful school mentoring programme - to help support some of our most vulnerable pupils to help them reach their full potential."