NTS said four chicks had hatched from one nest at the Mar Lodge Estate.
One male chick has been satellite tagged as part of the RSPB's Hen Harrier Life project.
The species was pushed to the brink of extinction by the early 1900s. Numbers recovered but there are still only about 500 breeding pairs in Scotland.
The large raptors are found mainly in moorland areas.
Mar Lodge Estate property manager David Frew said: "It is fantastic news and really exciting to see these birds returning to the estate for the first time in living memory.
"We have worked hard to create an environment where raptors can thrive, and it is great to see that our approach to management is paying off."
Will Boyd-Wallis, from the Cairngorms National Park Authority, said: "We very much hope that the careful management undertaken by the National Trust for Scotland alongside other estates in the East Cairngorms Moorland Partnership and in the wider National Park will lead to many more pairs successfully returning to the area."
Blanaid Denman, from the RSPB's Hen Harrier Life Project, said the news was "amazing", given the "parlous state" of Scotland's hen harrier population.
She added: "National surveys show a 20% decline in just six years between 2004 and 2010 and east Scotland in particular has seen only a handful of successful breeding attempts in recent years.
"All this makes the return of hen harriers to Mar Lodge even more exciting and a wonderful cause for celebration."
From the end of the summer, people will be able to follow the tagged chick's adventures online via the Hen Harrier Life Project website.
In the meantime, Mar Lodge Estate is running an online poll to name the chick.

The 27-year-old signed a new contract with the Championship club in February, keeping him at the Madejski Stadium until 2018.
But the new deal includes a release clause of £1.2m for Gunter, who helped Wales reach the Euro 2016 semi-finals.
Hull's interest is believed to be on hold as they search for a new manager following the departure of Steve Bruce.
Injuries have left the club with only 13 fit players, and they said they would look to strengthen the squad in the "coming weeks".
Right-back Moses Odubajo is one of several important players currently injured, and Gunter is regarded as a potential replacement.
The former Cardiff City and Tottenham defender played in all six of Wales' games at Euro 2016 as they reached their first semi-final at a major tournament.
The progress of Chris Coleman's side in France meant Gunter was forced to miss his brother Marc's wedding.

Thirty-six year old Marie Low died in Ninewells Hospital after an incident in the city's Ballantrae Terrace.
She was found with serious injuries at about 14:55 on Sunday.
A 30-year-old is expected to appear at Dundee Sheriff Court on Tuesday. Police Scotland said there would be a continued police presence in the area. Tributes have been paid online to Miss Low by friends and family.
Her daughter, Shanice Low, wrote on Facebook: "R.I.P mummy I love you millions I can't believe your gone. I'm going to make you proud love you loads mummy."
Her brother, Kevin Low, added: "Love you sis - gone but never forgotten."
Several other friends have changed their profile photos on social media to images of Marie.
Her sister, Denise Low, said: "It was our dad's birthday yesterday - we can't believe this has happened.
"My sister was strong and beautiful and will be sorely missed by us all.
"She was one of the best people I knew.
"She was a very, very strong woman. She always looked great."
One friend has also started a crowdfunding page.
Rare hen harriers have bred successfully at a National Trust for Scotland (NTS) estate in the Cairngorms for the first time in living memory.
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