The operation is set up in a house across the street from Sam Chapman Public School.
The owner was given a licence to legally grow 146 plants for personal use, but many people have been complaining about odours coming from the home's venting system.
Parents say they've noticed the pungent smell of the plants on their kids' clothes after they leave the elementary school.
A meeting for the public was held Wednesday night at the elementary school to discuss the issue.
"I'm shocked that this is happening, I can't believe this," said one woman at the gathering. "How can you give a guy a licence to do this across the street from a school?"
A couple living in the house next-door say the odour given off by the plants is "unbearable."
Oak Ridges-Markham Conservative MP Paul Calandra attended the meeting and fielded questions from angry parents for well over two hours.
Calandra agreed the home-based operation should be closed. However, he added that shutting it down won't be easy.
The federal government moved last year to ban Canadians from growing medical marijuana at home.
But regulations limiting cultivation to commercial operators were put on hold because of an ongoing legal challenge by a group of patients.
Other complaints about smell
Last month, the tenants of a Mississauga commercial complex spoke to CBC News about the smell coming from a nearby commercial marijuana grow-op.
Jon and Jackie Messenger said the operation at a plaza near Royal Windsor Drive and Southdown Road is making it hard to do business.
They said they can smell the plants all day long inside the offices of their heating and air conditioning company.
In December, CBC spoke to a Vaughan man who runs a restoration business about a similar situation with a business next to his that's legally growing the plants.
Mario Bottoni said the smell has been making some of his staff feel sick.