A new production of the show, based on the classic children's novel, will be created in the Capital where it will run for five weeks before embarking on a UK and Canadian tour.
The Christmas show will end a run of productions that include Brendan Cole – Live and Unjudged, Billy Elliot – The Musical and Don't Stop Believin' – Songs From Glee.
Unveiling the line-up, John Stalker, chief executive of Festival City Theatres Trust, said: "I am very pleased we have been able to cram so much into the season and appeal to many different audiences."
The Secret Garden was first brought to life through the music of Lucy Simon, sister of pop legend Carly Simon, and the lyrics of Marsha Norman.
It won two Tony Awards when it opened on Broadway in 1991, before being revived by the Royal Shakespeare Company in 2000.
And it will be re-created at the Festival Theatre by a team that includes Andrew Lloyd Webber's preferred casting director, David Grindrod.
Mr Stalker said: "It is a pleasure to make something very special for our local audiences, and the fact that a show made around the corner will be seen around the world is great news for Scottish theatre."
Among other shows scheduled for this season is Don't Stop Believin' – Songs From Glee, which will run at the Festival Theatre from 26-29 September, to the delight of fans of the hit television show.
Strictly Come Dancing star Brendan Cole will also put audiences through their paces with an exciting new show for one night only on 6 June, also at the Festival Theatre.
At the King's Theatre, 2 Pianos 4 Hands will chart the journey of two aspiring concert pianists as they play their way towards achieving their dreams, on stage at the venue from 28 October-6 November.
Mr Stalker said: "I'm really pleased we have secured this show. I worked on it ten years ago and I have always hoped for a Scottish production.
"It will really appeal to a wide audience – it's moving and very funny and you don't have to know anything about music to enjoy it."
The King's will also play host to Calendar Girls and Punk Rock in September and Lark Rise to Candleford and Bedroom Farce in October, before closing the season with an annual pantomime – Jack and the Beanstalk.
The King's panto dream team of Andy Gray and Allan Stewart will be reunited, joining Grant Stott for a seasonal treat for all the family.
Other shows to be staged at the Festival Theatre will include Peter Pan in June, The Singing Kettle in July and Kris Kristofferson in August.
The Secret Garden runs from 9 December-8 January.
Tickets will go on sale on Monday.