In a deal that solves one of the most vexing dramas in the city’s arts scene, the Huntington Theatre Company has reached an agreement to take control of the BU Theatre on Huntington Avenue, with plans to invest upward of $60 million in improvements.

“Bottom line is the Huntington is here to stay on Huntington Avenue where it belongs,’’ Mayor Martin J. Walsh said to a round of applause from a crowd of roughly 200 overjoyed theater backers gathered at a press conference Thursday to announce the deal. “The Huntington is going to gain exclusive control over this historic theater where it’s been for over three decades.’’

The announcement ends months of speculation about the fate of the theater, whose future was in doubt after Boston University announced last fall that it would be selling the building and two adjoining properties.

Michael Maso, managing director of the Huntington Theatre, said that under the terms of the agreement with the development group QMG Huntington, LLC, which purchased the three buildings for $25 million, the Huntington will be responsible for restoring the theater, which will abut a new mixed-use development that comprises both retail and residential units.

“We have a great deal of planning to do, and then we will have a great deal of money to raise,’’ said Maso, who estimated the theater company will need between $60 million to $70 million. “We can and we will fulfill the vision that this agreement makes possible.’’

Boston-area developer John Matteson, who represents QMG, said the development group plans to tear down the two buildings that adjoin the BU Theatre to make way for a new high-rise. He said it was too soon to say how tall the building would be, but he estimated the project would take 36 months to complete. He added that a portion of the first two floors of the building would house expanded amenities for the Huntington, such as a larger lobby and possibly a café.

“We always knew there would be a theater,’’ said Matteson. “Very quickly — within a day or two — we realized that the plan was to maintain the existing property and renovate it.’’

Matteson said the QMG Huntington group includes Boston-area developer Steven Goodman, who founded GFI Partners, and Fan Du, who manages Qianlong Property Development. Though the parties are still negotiating some of the terms of the arrangement, Matteson said the Huntington would likely enter a long-term lease for the theater.

“They’ll have 99 years with options,’’ said Matteson. He added that the theater company would likely pay a nominal, one-time rental fee, but in turn would be responsible for any future maintenance on the property. “It’s like they pay us a dollar and we don’t talk to them again,’’ he said.

The new arrangement will give the Huntington complete control over the theater, which it has used for the past 34 years in a rent-free arrangement with BU. The school also used the space to host other productions. During that time, it donated more than $40 million to the Huntington in subsidies and in-kind donations, according to Gary Nicksa, BU’s senior vice president for operations.

That relationship ended last October when the university began seeking bids on the .76-acre property. Though the Huntington made an initial offer to purchase the buildings, BU rejected the bid. In March, the university signed an agreement to sell the 890-seat theater and neighboring properties to Matteson’s group. The sale was finalized in early May.

Meanwhile, City Hall made no secret of the fact that it wanted the Huntington to remain on Huntington Avenue.

“My office got involved right away,’’ said Walsh, who hailed the agreement as a model for future public-private partnerships. “We did it because of the importance of this theater, the history here both nationally and internationally.’’

Maso said the 90-year-old theater has years of deferred maintenance, including a lack of women’s restrooms, a superannuated heating and cooling system, and a medieval electrical system.

“There’s a mouse and a treadmill back here,’’ joked Maso. “This is an old, old building.’’

Peter DuBois, artistic director for the Huntington, said that plumbing problems caused the orchestra pit to flood during a performance of “A Little Night Music’’ last fall.

Maso noted that while the estimate of $60 million to $70 million is steep, the Huntington raised some $24 million to build the Calderwood Pavilion, a South End theatrical complex that offers rehearsal and performance space to small- and mid-size theater companies at subsidized rates.

Under the new agreement, the Huntington will have to find new buildings for its scene, paint, and prop shops, which are currently housed in the buildings that adjoin the BU Theatre. DuBois and Maso estimated that renovations to the playhouse will take roughly 12 months. They said the company will have to perform in alternative venues as they update the theater, which will likely occur during 2018-19 season.

One possibility DuBois and Maso mentioned was the Colonial Theatre, which Emerson College says will remain a working playhouse after controversial plans surfaced last fall for the venue to be transformed into a flexible dining hall/performance space.

“My goal for that year is to think about it as an adventure,’’ said DuBois. “We can do things in very nontraditional spaces. We could do joint productions. There are a lot of different opportunities for audiences. It will be like a theatrical scavenger hunt.’’

Malcolm Gay can be reached at malcolm.gay@globe.com. Follow him on Twitter at @malcolmgay