Chris Gard and Connie Yates have announced their decision on a fund-raising website following Charlie's death.
The couple had appealed for cash to cover Charlie's medical bills on a GoFundMe page more than six months ago. More than 84,000 people have donated money.
"Our beautiful Charlie has been blessed with hundreds of thousands of supporters from around the world. We are so incredibly grateful for all your continued love and support, and would like to take this opportunity to advise you of what we shall be doing with the money raised for Charlie's cause," said the couple in a statement posted on a GoFundMe page.
"In the following weeks we will be setting up The Charlie Gard Foundation: a foundation that will help other children with mitochondrial diseases, and rare childhood illnesses.
"Too many children are losing their fight against rare medical conditions, which emphasises the need for more research, and we hope we can help deliver this through Charlie's foundation.
"We also intend on becoming a hub of information for parents that may find themselves in a situation like ours. There needs to be more clarity for parents about parental rights when it comes to making life-saving decisions about their children.
"Access to medical treatment, and expert clinicians, should never be denied if funds are available. We will be looking at ways in which we can help make things clearer for families and hospitals alike.
"We feel that the foundation will be a lovely legacy for Charlie, and we hope that you will all continue to support us in honouring the life of our little warrior as he helps other poorly children and their families."
Charlie died on July 28 shortly before he would have been a year old after his parents lost a high-profile treatment fight.
The little boy suffered from a rare inherited disease - infantile onset encephalomyopathy mitochondrial DNA depletion syndrome (MDDS).
Doctors caring for him at Great Ormond Street Hospital in London said life support treatment should end.
But his parents wanted him to be given an experimental treatment by a specialist in New York.
A High Court judge ruled in favour of Great Ormond Street doctors and said Charlie should be allowed to die with dignity.
Charlie's parents failed in a series of attempts to overturn Mr Justice Francis's decision.
The couple said GoFundMe had given £10,000 towards the foundation.
"It ... gives us great pleasure to announce that GoFundMe.com have been so touched by our cause that they have kindly donated £10,000 towards Charlie's foundation," they said.
"A wonderful gesture from the team, and we are extremely grateful for their generosity.
"All existing donations from our GoFundMe fundraising account - and any new donations - will now go towards Charlie's foundation."