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Urban Dove's website features a clock that is counting down to the first day of classes at the nonprofit's new charter school.

For most of this spring, Urban Dove Team Charter School’s story followed a familiar trajectory.

When the Department of Education offered the charter school space in a public school building, the community erupted in opposition. Politicians stepped in, principals went to the press, and parents protested — all with the goal of keeping the charter school out. Then the city signed off on the co-location anyway, and tensions started to die down.

That’s when Urban Dove’s story took an unusual turn. Despite getting free public space — a hotly sought-after commodity — Urban Dove signed a lease this month to spend some of its scarce per-pupil funding on private space. Next month, the transfer high school will open on one floor of Bedford-Stuyvesant’s Brooklyn Tabernacle Church.

It was a rare move for a charter school offered a public building. Most charter schools prefer to open in buildings owned by the city to save money and time spent negotiating with landlords, according to James Merriman, director of the New York City Charter School Center. Plus, money for real estate comes from charter schools’ operating budget — meaning the more they spend on space, the less they have for teachers, supplies, and programming.

Urban Dove’s founder and principal each declined to share the terms of the lease. But they said undertaking the significant expense made perfect sense for the school, which will serve students who have already fallen behind before they turn 16.

That’s because physical activity is central to the school’s curriculum, but the space the city offered — in Bed-Stuy’s M.S. 117 building, which already houses four schools — “barely had a gym,” said Principal Marianne Rossant. In fact, Rossant said, the school had sought the space at Brooklyn Tabernacle in the past.

The school won permission to open in 2011 but spent an extra year preparing to launch. One complication was that the school failed to find space in District 22, the Brooklyn district where Urban Dove originally aimed to open because it houses a large city park.

In the new space, the school will have a double-sized gym as three other rooms that will be used for core exercises, pilates, and yoga — more robust physical education facilities than many city schools can offer. And although Rossant said she and the other principals at M.S. 117 had begun to work well together once space sharing was approved, she is relieved to not have to worry about the intricate scheduling for gym time that co-location would require.

“Starting a school is a delicate, sensitive process and without the distractions of sharing a space, it’s much easier to accomplish,” Rossant said.

Urban Dove’s decision is good for the rest of the schools in the M.S. 117 building, too, according to a spokeswoman for City Councilwoman Leticia James, who was at the forefront of opposition to Urban Dove’s co-location.

“I think it was a disservice to both the school moving in and the schools already there,” said the spokeswoman, Barbara Sherman.

Urban Dove’s decision might be one that more charter schools could soon be compelled to make. The Bloomberg administration has readily handed public school space to charter schools, which are publicly funded but privately managed, allowing the sector to flourish. Now, about two-thirds of the city’s 140 charter schools operate in public space, paying nothing for the privilege. Charter school advocates are concerned that the successor to Mayor Bloomberg will not continue the controversial practice, making it harder for charter schools to open and operate after next year.

Merriman said the number of schools operating in private space is rising as real estate agents and brokers become accustomed to the charter school market. And many of the schools in private space say the flexibility and independence of their arrangement is more than worth the price tag, which can top $1 million a year. But very few schools have opted out of public space when it is offered.

For Urban Dove, the first year’s expenses will be defrayed by a $100,000 facilities grant from SUNY’s Committee for Education, College Readiness, and Success, awarded to the school even before it decided to move into private space. But Rossant said the sudden change in location would still require creative budgeting and some cutbacks. Some costs might be saved by using online resources instead of buying textbooks, she said.

One thing that won’t be skimped on is the school’s core mission, said Rossant and Jai Nanda, who founded the Urban Dove nonprofit in 1998 to empower city students through sports and recreation.

Nanda first conceived of the idea for a sports-focused school as a teacher and basketball coach in the 1990s, when he noticed that basketball players did better academically during the season, abetted by the rigid structure of their day and the support network of a team and coach.

At the school, students will be assigned to single-gender “teams,” replete with a coach whose sole job is to support the team throughout the day, which runs from 8 a.m to 6 p.m. The coach will motivate them on the field during three hours of fitness activities and health education each day, and follow them to class for the rest of the time.

The structure is meant to catch struggling students before they fall further behind. Urban Dove will open in September with both freshmen and sophomores who are already overage and under-credited for their grade. Few schools target those students, Nanda said.

“We’re getting them young enough to have meaningful change in the way they view school and themselves,” he said.

Rossant said she hopes the unique structure will keep students out of trouble after school hours, because they won’t need to turn to gangs for a sense of belonging — and because they’ll be exhausted from the long day. She also said she thought that the team spirit that the school’s structure is meant to foster would be paramount to students’ success.

“You can let an adult down — that’s par for the course as an adolescent,” she said. “But you don’t let down your friends, your group.”