The incident, at a school in Dundee, is being looked into by police.
Grace Simpson, from Menzieshill told a local newspaper: “I am appalled. This incident has come at the end of a year and a half of bullying of my son.
“I have removed him from the school and I have reported the matter to the police.
"My child will not be returning and I have asked Dundee City Council to place him in another school.”
The 33-year-old sad her son has been subjected to bullying including footprints left on his back from being kicked and bite marks.
Grace said: “For the past year and a half my son has been horrifically bullied by the same boy. This culminated on Thursday with this boy threatening my son with a pair of scissors . He approached James with scissors in his hand and threatened to stab him.
“Fortunately he was unharmed but only because the class teacher managed to get between him and this other boy.”
“The school refused to remove the boy from the class so they were separated.
“All they have done is have conversations with the boys making the bully listen to how he makes my son feelThat’s all the punishment he has received.
“I am absolutely disgusted that this bullying has been allowed to continue.
“I want action taken now to protect my child and others. I detest bullying of any sort and this has now gone way too far."
A Dundee City Council spokesperson said: “We are not able to comment on any individual cases but all complaints about bullying are taken extremely seriously.
“Families are always involved in the process.
“If any parent has concerns about their child at school they should discuss these directly with staff.”
Police Scotland has confirmed it is looking into the matter.