The two organisations said they hoped the arrangement would enable them to support more young people and have a greater impact in geneal.
The deal marks the first time the Scout Association, which has more than 600,000 members in the UK, has been involved in delivering the NCS.
A statement from the two organisations said the partnership would be the first of many to test ideas through the NCS’s new innovation programme, which has been set up to enable the NCS Trust, which runs the scheme, and its partners to test new approaches to improving social cohesion, social mobility and civic engagement through the NCS.
The scheme offers 16 and 17-year-old school-leavers the chance to take part in seven or eight-week projects that include community work, a physical challenge and a residential placement.
The project, which is being supported by £1.5bn of government funds between 2011/12 and 2019/20, has struggled to fill all of its places and earlier this year it significantly reduced its participation targets.
The House of Commons Public Accounts Committee said in March that the high cost of the scheme could not be justified.
The statement from the two organisations today said the partnership would open up new opportunities for the Scout Association to deliver innovative NCS programmes and integrate the NCS experience within scouting.
A spokesman for the organisations said the precise work the Scout Association would carry out was still being worked out, but was expected to be finalised soon.
As part of the deal, the TV presenter and chief scout Bear Grylls will become part of the NCS board of patrons, which is chaired by the former Prime Minister David Cameron, who introduced the scheme.
Sir Stuart Etherington, chief executive of the National Council for Voluntary Organisations, said he hoped the deal would mark a turning point for the scheme.
He said the NCVO had been calling on the NCS for some time to work more closely with charities that shared its aims.
"Many in the sector feel the NCS has not worked well with local charities and not integrated itself well into local volunteering ecosystems," he said. "This has been frustrating for those organisations and a missed opportunity for young people.
"I hope today will mark a turning point in the NCS relationship with the voluntary sector. All these concerns are being addressed as part of its nascent partnership with the Scout Association."
Matt Hyde, chief executive of the Scout Association, said he hoped NCS graduates would become the scout volunteers of the future.
"Marrying the scale, reach and 110 years’ of experience of scouting with the resource and innovative delivery of the NCS will mean we have an even greater impact on many more young people," he said.
Michael Lynas, chief executive of the NCS, said: "This partnership means that young people from all backgrounds will benefit from NCS programmes delivered by the scouting movement, and NCS graduates can in turn help scouting to expand its work in some of our most disadvantaged communities."