Michelle Amey, 35, had brain surgery to remove a tumour, and without a car, will have to catch a bus to drop her sons off at their different schools.
She and her husband Stuart are urging Dorset County Council to find a place at Mudeford Infants school for their younger son, George, four. Older son Charlie, seven, is already at the school.
The council say they are out of the catchment area, and that George will be offered a place elsewhere.
Michelle branded their decision 'heartless', explaining: "It means with the way I am feeling I would have to walk George to school and then take a bus to get to drop Charlie off. One child would end up being late every morning and picked up late every evening. That would make our lives even harder. This would be hard enough for any mum let alone one in my condition."
Michelle first became ill soon after George's birth, when a mole turned out to be a malignant melanoma. The cancer eventually spread to her groin and she had surgery and radiotherapy.
Last April they were told that George did not have a place at Mudeford Primary where his brother is now in Year 2, and instead were offered two other schools further away - one of which is not served by buses.
The couple appealed the council's decision at the time, but were turned down on the basis that Michelle could drive if needs be, but just before Christmas last year, Michelle was told the cancer was in her brain, liver and adrenal gland.
She said: "Because the cancer was in my brain I cannot drive for two years so my circumstances have changed. But we went back to the council and got a very nasty email back saying nothing has changed in their mind.
"It reduced me to tears.
With things as they are, the boys need each other for support. They are best friends and it is very important for them to being able to support each other at school at a time like this.
The family say the council offered to get George a taxi to school each day, but he would have to travel alone. His dad said this was ridiculous for such a young child: "I don't know anyone who would let their four-year-old travel alone in a taxi."
Mudeford Infant school headteacher Duncan Churchill said 'it is a really unfortunate situation' but that admissions were dealt with by the local education authority and not the school.
Dorset County Council's director for children's services, John Nash said: "To admit another child would exceed the 'class size of 30' legislation."
The couple have started a petition appealing for Dorset County Council and Education Secretary Michael Gove to overturn the decision.
Surely they could find a place for this little boy in these exceptional circumstances?