FOTSN has become a restricted fund within the Archie Foundation and will retain its own brand identity as part of the move, which came into effect yesterday.
David Cunningham, chief executive of the Archie Foundation, will be chief executive of the new organisation.
He said the two charities delivered very similar services in north-east Scotland and it therefore "made sense for that to be better coordinated".
There have been no job losses as a result of the merger, said Cunningham. The Archie Foundation employs 20 staff and FOTSN was run by volunteers.
He said all of FOTSN’s assets had been transferred to the Archie Foundation.
The FOTSN board has been dissolved, but the charity has appointed two trustees to the Archie Foundation’s board.
Cunningham said: "By working together we can make a bigger difference in a more efficient way. We will be able to ensure that all our beneficiaries, and our donors, receive the highest possible care and support."
Kirsty Mills-Bishop, chair of FOTSN, said: "Friends of the Special Nursery is a wonderful fundraising group, run by parents whose own babies have spent time in the neonatal unit and by staff who are incredibly dedicated. They have done a great deal to help babies and their families in the unit over the years and we will continue to do exactly that.
"However, we will now do that as a fund within Archie, which allows us to enhance our governance, better coordinate our expenditure and share our expertise to maximise the impact for local families in need of our support."