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The days of Boston families signing up their children for the Metco program as soon as they are born are now history.

Massachusetts education officials have given the voluntary school integration program permission to choose students through a lottery instead of on a first-come first-serve basis, in an effort to bring more fairness to those who get in. Under the changes, announced Monday, parents will be able to submit applications only in the fall for the following school year.

“This is a very historic moment for Metco,” said Milly Arbaje-Thomas, chief executive of the Metropolitan Council for Educational Opportunity, which runs the program. “We now will be able to meet all constituencies in all neighborhoods, whether they are long-term residents or newcomers. We want a student population that is more reflective of Boston’s demographics.”

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The new system, which was originally proposed earlier this year, will be phased in over the next two admission cycles, starting with students seeking slots for the 2020-21 school year. Applications will also shift from paper to an online portal. Families, however, will still be able to apply in person at the program’s Roxbury office.

Metco, which enrolls 3,300 Boston students in 33 suburban districts annually, has often been held up by researchers and policy makers as a successful way to voluntarily integrate public schools. A Harvard University researcher this winter found that Metco students had higher high school graduation rates and college enrollment rates than their peers in traditional Boston Public Schools and charter schools.

The children are bused from Boston to the schools in the suburbs. The state spends about $20 million annually to fund Metco in Boston and another program in Springfield, although suburban districts spend their own money on the program, too.

The program’s success has fueled a fever-pitched frenzy to get in, resulting in a waiting list of 15,000 students, about half of whom were infants or toddlers. Program staff filed away paper applications in the order they were received and for the specified school year.

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But the program also has been plagued with questions over the fairness of its application process and whether it is truly serving students with no other options. That’s because the program tends to enroll a student population that is more affluent than the one in the Boston Public Schools.

The program also has failed to keep pace with the changing diversity of Boston, enrolling mostly black students at a time when the city has seen a big infusion of Latinos and other ethnic and racial groups.

The state Department of Elementary and Secondary Education formally approved the new application process on April 30. The program has largely purged its waiting list.

“We appreciate the thoughtful approach that Metco Inc. has taken, and we believe these changes will help bring clarity to the Metco enrollment process in Boston,” said Jacqueline Reis, a state education spokeswoman.

Families hoping to secure seats for their children for fall 2020 can apply between Oct. 2 and Dec. 31. The lottery will take place in January. Children who don’t win a seat will need to reapply for a subsequent school year.

The changes initially generated concerns at a public forum in February among some families who had their children on the waiting list.

In response, Metco decided to give priority status to hundreds of children who had been on the waiting list for admission for the 2020-21 school year. For students on the kindergarten waiting list, the program will refer their applications to suburban systems in the order they were received.

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For students on the waiting list for grades 1-12, those applications will also be referred to the suburban districts in the order they were received. Both groups will still need to fill out an online application this fall to preserve their wait-list priority status.

Metco will rely strictly on the lottery for subsequent years. Siblings of students currently enrolled in a suburban system will have priority. The Boston Public Schools has a similar policy on sibling preference for its student enrollment process.

Darnell Billings, a parent representative on the Metco board who also attended the program as a child, said the changes to the application process are a step in the right direction.

“Metco is trying to . . . make sure things are transparent, so it’s an even playing field,” said Billings, a Boston resident whose son attends the third grade in Lincoln through Metco.

Metco will be designing the online application this summer and is working with SchoolMint, a California-based company that also is used by the Boston school system and most Boston charter schools for their online school applications systems.

More changes could be on the way. Arbaje-Thomas said the program will be drafting specific admission criteria. Currently, the program refers applicants to specific districts, which have some discretion in making admission offers.

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“We are trying to keep the program viable and alive for another 50 years,” she said. “In order to do that you have to modernize.”


James Vaznis can be reached at james.vaznis@globe.com. Follow him on Twitter @globevaznis.