One of the city’s oldest and highest-performing charter schools is being evicted by an unlikely landlord: the community organization that founded it.

Harbor Science and Arts Charter School, which opened in 2000, will have to find a new space in coming years after Boys & Girls Harbor, a 74-year old nonprofit that serves East Harlem youth, told the school’s board that it was ending an 11-year partnership.

The sudden news has jolted school administrators and unnerved families — and also illuminated a strange irony: While charter schools are sometimes criticized for disrupting other schools’ space, they too are at the financial and operational mercy of their landlords if they rent private space, as Harbor Charter does.

For Harbor Charter, which has paid $150,000 a year for use of two floors in the nonprofit’s building and access to its pool and gym, the shift could come at significant cost. Some charter schools in private space spend up to $1 million annually for their facilities.

The “decision to dissolve its current partnership/relationship” was Boys & Girls Harbor’s alone, according to a letter that Joanne Hunt, Harbor Charter’s principal, sent to parents last week. In the letter, Hunt assured parents that the school’s existence was not in jeopardy and that it planned to stay in the district. But she said she did not know where it would be located next year.

“We are confident that this separation will be a positive one for the charter school,” Hunt wrote in the letter. “Change is uncomfortable, but at times it is necessary.”

Hunt’s assurances weren’t enough to calm all parents, who sought additional answers at a PTA meeting Thursday night.

“We want to know why,” said Steven Greene, whose daughter is a seventh-grader at the school, before the meeting. “Why are you pushing out the charter school?”

A clue can be found in Boys & Girls Harbor’s evolving educational mission, according to the school’s board chairman, Alvin Patrick. When the school opened in 2000, the school’s board and the Boys & Girls Harbor board were basically made up of the same people, he said.

Initially the school struggled, but it stabilized after Hunt took it over in 2002, according to a trajectory of annual reports from the school’s authorizer, SUNY’s Charter School Institute. Since then, the school, which enrolls 240 students in kindergarten through eighth grade, has twice had its charter renewed, boasted a near perfect student retention rate, and has mostly outscored other schools in its district on state tests.

As the school improved, the relationship between the two boards “evolved, with the school becoming more independent,” Patrick said. Now, just one of the 25 members of Boys & Girls Harbor’s board, its executive director, also sits on the school’s board.

“The current [Boys & Girls Harbor] board said that they wanted a more inclusive role in the relationship beyond a landlord and back-office support role, and they did not foresee a more inclusive relationship in the future,” he said.

Leadership changes at Boys & Girls Harbor might well have heightened the tension.

In recent years, William Ackman, a hedge fund CEO who has recently plunged into the world of education philanthropy, has become a more prominent figure on the board. Ackman, the founder of Pershing Square Capital Management, joined the board in 2005, became real estate chair two years later, and is now the board’s president. His commitment to education issues seems to have deepened in recent years. In 2010, his firm’s foundation donated $25 million to Newark Mayor Cory Booker’s school reform efforts and in early 2011 he led fundraising efforts for an event to benefit Boys & Girls Harbor.

In 2010, Hans Hageman resigned from Boys & Girls Harbor after nine years as executive director, a period in which he oversaw the charter school’s turnaround. Hageman was replaced with Thomas Howard, a former music teacher and principal. Howard’s most recent job was chief academic officer of Victory Schools, Inc., the city’s first charter schools network, which rebranded itself in 2010 after a new law barred for-profit companies from operating or managing charter schools in New York State.

In an interview, Howard praised Harbor Charter and said the decision to part ways with the school was less about controlling its operations and more about controlling the nonprofit’s longterm strategic vision.

“It’s about strategic growth within the organization,” he said.

Howard said the organization would focus on expanding its early learning programs, from serving 85 children to “several hundred.” He also said the organization was looking into “other education partnerships to expand the number the students we serve.” He would not specify if Boys & Girls Harbor might try to host another new charter school.

Howard said that both board are working together on a transition and that Boys & Girls would continue to support the charter school until at least the end of the school year and as late as September 2013 as the school seeks new a space — which Patrick said it has already started doing.

“District 4 is where we want to be and the move will happen when we find the right space,” said Patrick, who added that a public school building could be an option. “We’ve been in contact with the DOE, but we’re also looking at private spaces. We just don’t know.”