The evaluation of ROADS II, a charter school in the Bronx, is peppered with compliments about the school’s leaders and their ability to help at-risk students.

Yet ROADS II is also failing by a basic statistical standard: Almost none of its students graduate within four years.

The school is one of a handful of charter schools that serve a subset of New York City’s neediest students, often those who are over-age and under-credited, homeless, or in foster care. Like all charter schools, it is expected to meet strict standards or face closure.

Yet schools like ROADS II present a tough question for the authorizers that oversee them: What happens when serving an important group of students makes it nearly impossible to meet normal benchmarks?

“I think it makes sense they hold the bar high,” said Jemina Bernard, the chief executive officer at ROADS. But, she said, “If it takes them five, six years to [graduate], it’s not anything that we’re ashamed of.”

The city has long grappled with similar questions about how to measure its non-traditional schools. Now, the State University of New York Charter Schools Institute, which oversees more than 100 charter schools in New York City, is facing a deadline to tackle the problem. Three charter schools serving especially high-needs students — Broome Street Academy, ROADS I, and ROADS II — are up for renewal this year and next.

Susan Miller Barker, the institute’s executive director, said that officials there haven’t yet come up with exactly how those schools will be evaluated. But they are working to adjust SUNY’s focus on graduation rates and test scores to determine whether these schools are performing well.

“We think that all kids coming out of high school ought to have a high school degree,” Miller Barker said. “But we’re looking at them and saying, is there something else that would tell us how well the schools are doing?”

The current guidelines set a high bar. Charter schools are generally expected to aim for 75 percent student proficiency on state exams, for 75 percent of their students to graduate in four years, and for 95 percent to graduate within five years.

Those numbers, charter school operators and advocates said, are unreasonable for schools designed to take in students who are older than their peers and have already struggled to make progress in school.

For example, high school students learning at a middle school level might make years of progress, but that growth is invisible if measured only by Regents exams designed for high school students, said Leslie Talbot, an education consultant and a leader of the Pathways to Opportunity Project, which focuses on helping off-track youth.

The benchmarks for credit accumulation and graduation timelines are also troublesome.

At John V. Lindsay Wildcat Academy Charter School in lower Manhattan, the majority of students are over 16 and have earned fewer than nine credits, according to principal Ron Tabano. For them, graduating within six years is difficult and within five is nearly impossible, he said.

Instead, Wildcat Academy, which is overseen by the city’s education department and was converted into a charter school in 2000, has historically been compared to the city’s other transfer schools. Its six-year graduation rate, not the four-year rate, is tracked over time.

“There has to be a different set of measures,” Tabano said. If schools like his were punished for not graduating students in four years, he said, “They’d get killed.”

In 2011, the Bloomberg administration adapted its school letter grade system and progress reports for transfer schools, focusing on six-year graduation rates. The de Blasio administration did not release its own school “snapshots” for those schools last year, but the education department is looking to account for factors like student homelessness in its reports for all schools.

Schools like Broome Street, which gives preference to students who are homeless or in foster care, also help the charter sector combat the perception that it doesn’t serve its fair share of the highest-needs students. Chancellor Carmen Fariña has criticized charter schools for serving lower-than-average numbers of special education students and English learners but praised Broome Street — even speaking at its graduation ceremony this year.

SUNY’s challenge now is sticking to the essential bargain offered to New York charter schools — outperform traditional schools or be closed — without discouraging prospective school operators from trying to find new models to serve needy students.

The trick, New York City Charter Center CEO James Merriman said, is to engage in “smart accountability,” or finding reasonable standards for schools that need alternatives while ensuring that they don’t become a veiled effort to protect schools from accountability.

“This is not easy to do,” he said.

As SUNY works toward decisions about new measures, it also must decide which schools qualify for them.

States like Colorado, Texas, and Arizona have defined alternative charter schools and created separate accountability standards for them in law, said Jim Griffin, president of Momentum Strategy and Research, an organization that works to improve charter school accountability. New York does not have such a clear formula, he said.

For now, SUNY appears to be looking at schools designed from the start to serve special groups of students. Officials say they may focus on measures like attendance rates, student progress towards graduation, or even the support offered to students who are parents or who are involved in the court system, though graduation rates and state test scores will remain important.

“If you want to run a charter school, you agree to being measured based on how well you prepare students to succeed when they leave you,” Miller Barker said.