The warning comes in a letter from the Simon Fraser Society for Community Living that could affect more than 1,000 B.C parents.
Anne Belanger's eight-year-old son has a condition that makes him completely physically dependent on others.
Belanger assumed the province would pay the boy's daycare bill if there was a strike, as has happened in the past.
But then she received a letter from her daycare.
"It just said there is no money," said Belanger."There is no funding."
However, the letter does say there is money available for parents like Belanger outside of normal school hours under a different funding arrangement. There's just no money during regular school hours, if the strike continues into September.
"While we hope that the issues between the two sides will be worked out over the course of the summer, should the job action go into September we will not be able to fund the additional hours," says the letter from the Simon Fraser Society for Community Living .
"So, with brief calculations, if school doesn't go back in September, my monthly daycare cost will reach more than $3,000," said Belanger.
No final decisions on daycare says province
Belanger says an education assistant is with her son all day during the school year. Over the summer, the province pays for his daycare support, but now she doesn't know what she's going to do.
"Do I pay for childcare and just basically take my pay cheque and burn it, or do I stay home and try to put a roof over my head and feed my family?"
Other parents of special needs children are asking the same question. Annette DeLaplace is concerned for her 17-year-old daughter, who is confined to a wheelchair.
"If school isn't back on September 2nd, my daughter will be home with me, and I'll be home from work."
But the province insists no final decisions have been made on what will happen to daycare funding in the event of a strike.
B.C.'s Education Minister says that's one of the reasons it's so important to reach an agreement with teachers.
"We want to deal with the future of education; to meet the need of every single student, whether they have special needs or whether they're gifted and everything else that might be in between that," he said.
"To get there, we have to have a closer and better working relationship with the key element and that is the teachers."
Fassbender is holding out hope a deal can be struck before classes are scheduled to start, but there is currently no bargaining taking place.
The B.C. Teachers' Federation says Fassbender's is playing politics with his public comments under what is supposed to be a media blackout.
"Today, I am calling on Peter Fassbender to honour the media blackout and instruct BCPSEA to immediately begin intensive mediation with the assistance of Vince Ready," said BCTF President Jim Iker in a statement.
"The BCTF bargaining team is ready at any moment to begin this important work. Teachers hope the government is finally ready to compromise to get a negotiated settlement."