There had been doubts about the facility after the 15 million appeal descended into chaos earlier this year and ultimately closed.
But it is understood several organisations will club together to make sure the facility is built, with NHS Lothian also reiterating its confidence that the original funding target will still be reached.
In the absence of the New Pyjamas appeal – which was run by the Sick Kids Friends Foundation – six charities will shoulder responsibility for the unit.
Those are Ronald McDonald House, CLIC Sargent, Teenage Cancer Trust, Trefoil House, Snowball Trust and SNIP.
Jackie Sansbury, NHS Lothian's director of strategic planning and modernisation, told board members at a recent meeting that, despite the demise of New Pyjamas, accommodation for relatives was "secure".
It comes as a boost for the hospital project, which has been dogged by the high-profile chaos of the New Pyjamas appeal, which wound up making all its staff redundant in the wake of Evening News revelations that it had raised only 60,000 since its creation, despite spending 500,000.
Ms Sansbury added that she "remained optimistic around the ability to raise 15m through an appeal and had not changed the project plan".
It is expected a similar appeal will be launched between NHS Lothian and the SKFF later this year, but question marks still surround other initiatives pledged by New Pyjamas, including internet access for every child, classrooms to help patients continue schooling if they are in hospital for a lengthy period and a much anticipated drop-in centre for families to relax in.
An NHS Lothian source said: "It is fortunate that there are so many charities willing to help this project because it really could have been up in the air.
"It's something of a new feature for hospitals but it is things like the hotel that sets a hospital apart from the rest, and it's one of the first projects people were worried about when they heard about the problems at the SKFF."
CLIC Sargent already runs a "home from home" facility near the existing Sick Kids at Sciennes which is one of the most popular aspects of the hospital, and it is expected that organisation will be a main player in the new project when it opens in 2013.
Morag McIntosh, head of fundraising for Scotland, said: "We wanted to build a home from home at Little France but there was no room, so we will take a floor of the hotel. It will be about the same size as our current one and the funding is already in place."