Six decades ago, the Supreme Court’s unanimous Brown v. Board of Education decision sought to ensure that all children had access to good educational institutions. With the civil rights movement’s continued emphasis on education as central to economic freedom, 48 years ago the Metropolitan Council for Educational Opportunity (METCO) desegregation program was established to serve Boston and Springfield.

Today, as Boston public school students head back to school, many will experience the city’s new school assignment process, which shaves about one-tenth to two-tenths of a mile off the daily trip to school for kindergartners and pre-kindergartners. Meanwhile, 3,000 Boston METCO students will continue to travel five, 10, even 25 miles to attend public schools in Brookline, Lexington, Sherborn and other suburbs.

METCO is part of the seldom told story of school choice in Boston. Over one quarter of the 77,000 school-aged children residing in Boston study in alternatives to the Boston Public Schools (BPS). If you include students on charter school and METCO waitlists, more than half of the students in Boston want an option other than BPS’ 128 “district” schools.

More than three-quarters of METCO students are African American or Latino. Half come from low-income families; one in four has special needs.

Parents opt out of Boston’s district schools for many reasons. Some do so because the district’s MCAS scores are 15 to over 30 percent below and SAT scores are 70 points below statewide averages. Others seek safer environments or schools that instill a different kind of values-based education. While all prefer choices closer to home, parents operate from the knowledge that only a third of BPS schools perform adequately, and that the chances of getting a child into the district school of their choice are not high.

METCO has an appealing story for Boston parents. The commonwealth’s Executive Office of Education reported a 94 percent four-year high school graduation rate for METCO students in 2011, compared with 85 percent statewide, 64 percent in Boston and 52 percent in Springfield. Of these graduates, 89 percent of METCO students enroll in higher education, compared with 81 percent statewide, 59 percent in Boston and 67 percent in Springfield.

Despite its success, since Gov. Deval Patrick took office, state funding for per-pupil METCO expenditures has fallen by 18 percent, even as school spending in METCO receiving districts has increased by a third. This school year, receiving districts will only receive $3,581 per student to cover all METCO-related expenses, including transportation and METCO program staff. Once those costs are factored out, receiving districts may receive less than $2,000 as reimbursement for the education of each METCO student, even as actual educational costs per student range between $15,000 and $20,000.

With student enrollment growing fast across Boston’s suburbs and “excess” seats hard to find, the districts that serve METCO students find this mismatch of funding and expenditures increasingly unsustainable.

Underfunding is not the only threat. METCO is currently funded by a state budget line item that is separate from other K-12 spending, which means the program must fight for its life during each annual budget debate.

The educational establishment has long turned its nose at METCO. The state’s department of education prefers to tweak the monolithic district system, through such reforms as the BPS’ three dozen pilot schools, in-district (unionized) charter and innovation schools. These efforts have produced a few interesting, higher-performing outliers, but as a whole they have not delivered results remotely comparable to METCO.

METCO can and should be improved. The program needs greater transparency in its selection of participating families, better supports for those families, and better tracking of students’ enrollments and persistence in college.

While it may need a tune-up, METCO deserves more funding and attention from the state.

Together with commonwealth charter schools and — hopefully — new mayoral energy behind giving Madison Park Vocational-Technical School autonomy from the BPS system, METCO is a vital and empirically proven way for Boston to expand the next generation's economic mobility and freedom.

Jim Stergios is executive director of Pioneer Institute, a Boston-based think tank that focuses on issues related to social mobility and economic freedom.