Ellie Mae, five, and Caleb, three, may not live to see their teens after they were both diagnosed with Late Infantile Batten Disease.
The condition is so rare that only five new cases are diagnosed every year in the UK.
The disease, which starts at around the age of three, will see the siblings eventually lose their mobility, speech and eyesight.
And doctors have said it is very rare for children with the condition to survive into their teens.
The devoted parents, who were given the devastating news just one week before Christmas, are planning to make the most of their time with their children.
The family from Cookridge, Leeds, are looking forward to a family holiday in Disneyland, in America, this summer thanks to a generous collection raised by Mr Brownutt’s colleagues.
Their mother, 35, said: “Children with Battens can’t play or talk and they will lose all of that.
“It’s just like your worst nightmare and we just have to take it day by day. I can’t think too much into the future.”
Mr Brownnutt added: “The best case scenario is that they will get to their mid-teens. The worst case, most horrible scenario is that we have got another five years with Ellie Mae.”
The family realised there was something wrong when Ellie Mae started with epileptic seizures at the age of three.
Just one month before her fifth birthday she lost her mobility.
Her brother Caleb is full of energy and loves nothing better than playing football.
But his parents fear it will be a matter of time before he is confined to a wheelchair.
Mrs Brownnutt said: “It will be really hard when he loses his mobility.”
Mr Brownnutt, who is a store manager for Vodafone, added: “We have got pictures of Ellie Mae on her first day of school in her uniform and she walked to school that day. One month later she couldn’t walk at all.”
The devoted father is currently enduring a 150 miles of pain challenge to raise money for the Batten Disease Family Association, which has become a support line for the family. He is running five miles every day for a month, has raised thousands of pounds for the charity.