Two River Public Charter School pre-K students take part in physical education class in the common area known as “The Greens” in 2012 in Washington, D.C. (Mark Gail/The Washington Post)

A federal judge has ruled against an association of Washington, D.C., charter schools that for three years pressed a lawsuit alleging the city government was unlawfully providing more money to traditional public schools than to charters.

The lawsuit was seen by many in the District as a fundamental test of the city’s authority to govern itself using powers delegated by Congress through the 1973 Home Rule Act, and U.S. District Judge Tanya S. Chutkan acknowledged as much in her decision, dated  Saturday. While the city — which is not a state but a federal district subject to congressional oversight — has been granted the power to elect its governing body and set its own budget, Congress still has the right to step in, and it has.

To score points with constituents at home, conservative members of Congress have routinely overturned laws passed by liberal D.C. lawmakers. They have frozen funding for abortion coverage for low-income women, blocked money for a needle-exchange program and even kept the city from counting ballots cast by residents who voted to legalize medical marijuana.

Congress also created the only federally funded school voucher program in the country in Washington, D.C., and continues to fund it, even though a majority of the D.C. Council in 2015 wanted to eliminate it. The House recently voted to repeal the city’s new assisted suicide law.

In her decision, Chutkan rejected the argument made by two charter schools and the D.C. Association of Chartered Public Schools that the city government was violating the 1995 School Reform Act by failing to provide uniform funding for the two kinds of publicly funded K-12 schools in the District. The association serves all of the 120 charter schools — which are publicly funded but operated independently from the D.C. Public Schools system — in the nation’s capital.

A little more than half of the more than 90,000 public school­children in the city are enrolled in traditional public schools, with the rest going to charters. Charter schools, which are approved and overseen by an appointed board, were introduced into the city after the passage of the 1995 reform act, which mandated that the city create a “uniform formula” to fund charter and traditional schools based on enrollment.

The lawsuit alleged that officials had found other ways to unlawfully give traditional schools more money than charters, mostly through services from city agencies. The lawsuit reflected a longtime complaint from the city’s charter schools that the local government was underfunding them; it estimated that from 2008 to the time the lawsuit was filed in 2014, the city had spent about $2,150 less per charter school student each year than it did on traditional public school students.

The lawsuit was filed by the D.C. Association of Chartered Public Schools, along with Eagle Academy and Washington Latin public charter schools. In the fall of 2014, Chutkan rejected a request by the city’s attorney general to dismiss it, saying the plaintiffs had a “plausible claim for relief” and that “it is not yet clear whether the actions of the council impermissibly conflict with the will of Congress as set forth in the Home Rule Act and School Reform Act.”

The lawsuit challenged the funding on two grounds. It argued that the District had exceeded its authority under the Home Rule Act by enacting legislation and making budgetary appropriations that it said conflicted with the School Reform Act. It also alleged that the District’s funding decisions and practices violate the act’s requirement calling for a uniform funding formula.

In her new decision, the judge stated clearly that the District’s funding practices do not violate the School Reform Act and that the plaintiffs have “no standing to challenge the District’s enrollment calculation method for” D.C. Public Schools.

(Correction: An earlier version said the U.S. House had yet to vote on a bill to repeal the District’s assisted suicide law but that the House Appropriations Committee had passed it. The full House did approve it as a rider to an appropriations bill.)