In a statement released by the union, teachers at the K-8 charter alleged that foot-dragging by the board had prompted many staffers to leave, undermining students' learning.
Khepera's first union contract expired in December 2012 and was extended three times through last August as the teachers attempted to reach a new agreement.
"With negotiations dragging on nearly two years, staff turnover has been tremendous," Kim Johnson, a science teacher and president of the local, said in the statement, issued late Tuesday.
"Teachers want to provide the best education possible, but without a contract, many of our teachers are looking for jobs elsewhere so they can support their own families, pay their student loans, and apply for mortgages," added Johnson, whose children graduated from Khepera. "It's taking its toll on the close relationships that have been established between the teachers, the children and the parents."
Richard Isaac, Khepera's board president, could not be reached for comment Wednesday.
Teachers and some parents held an informational picket line April 10 to call on parents to urge Isaac to reach a new agreement.
The association has filed two charges of unfair labor practices against Khepera that are pending before the National Labor Relations Board, union sources said.
Khepera opened in 2004. Its five-year operating charter is up for renewal, and the district's charter office is reviewing the school's operations.
Although Pennsylvania's 1997 charter school law gives teachers the right to unionize, teachers at only a few charters have done so.
The alliance, an affiliate of the American Federation of Teachers Pennsylvania, also represents teachers at four other charters in the city.
Teachers at the Pennsylvania Cyber Charter School, the largest cyber charter in the state, recently voted to form a bargaining unit with the Pennsylvania State Education Association.
The online school based in Midland, Beaver County, enrolls more than 11,000 students from across the state.
PSEA has represented teachers at a few other charter schools in the past, but Pennsylvania Cyber is the only charter in the state now affiliated with that union.