A freedom of information request by the Scottish Liberal Democrats has found at least 2251 instances of racism in schools between the 2017-18 and 2019-20 academic years.
Glasgow City Council saw the highest number of reported incidents with 642, with reports in Edinburgh at 490.
Orkney recorded the lowest level of incidents with three, all of which occurred in 2017-18.
West Lothian, Highland and Falkirk councils did not reply, according to the Lib Dems.
The party’s education spokeswoman Beatrice Wishart said: “No-one should go to school afraid that they will face racist abuse but these figures show that racist incidents remain a stubborn stain on Scottish schooling.
“All forms of bullying need to be challenged effectively. That means accurate recording and monitoring of bullying so that the right interventions can be put in place to stamp these incidents out.
“The Black Lives Matter movement has encouraged us all to think about racial injustice and to reflect on Scotland’s own history.
“By and large, Scotland is a great place to live but learning the lessons of the past will allow us to do even better in the future.”
Debora Kayembe, an Anti racist campaigner and leader of the Freedom Walk campaign (pictured), outraged by the finding, reacted on her Facebook page. Watch video
A spokesman for the Scottish Government said: “Bullying of any form is entirely unacceptable and we need to be vigilant in challenging any racist and abusive behaviour in schools.
“Where it occurs, it must be challenged through educating children about all faiths and belief systems, ensuring they learn tolerance, respect and equality.”