Across Scotland there are now more than 500 children who are home-schooled compared to 350 in 2010.
Alison Preuss, a spokeswoman for the home education charity Schoolhouse, said bullying and worry about support for special needs pupils were the main reasons parents opted out.
"The inflexibility of the school system and its inability to meet the needs of individual children drives many parents to consider home education," she said.
Brian Donnelly, director of the Government-funded anti-bullying service Respectme, said it was unacceptable for families to be driven out of the mainstream system because of classroom conflicts.
"It is very disappointing that children are being taken out of school because they are the victim of bullying. It reflects a failure on everyone's part to find a solution," he said.
Liz Smith, education spokeswoman for the Scottish Conservatives, called on the Scottish Government to look at why there had been a rise in the past three years.
"It is very surprising to learn that there has been such a large increase. I would call on the Scottish Government to look into this," she said.