A new $90 million deal with the Archdiocese of Chicago is set to give a prominent Catholic foundation a major role in the operations of 30 area schools while giving the schools a lifeline to stay open for at least the next decade.

The agreement comes two weeks after the announced closure of another five Chicago-area Catholic schools, including one on the city’s Southwest Side, that the Archdiocese blamed on low enrollment and poor financial outlooks. The deal also comes in the wake of deep financial trouble for the Archdiocese, which is more than $200 million in debt mostly because of sex abuse claims.

Jim Rigg, superintendent of Chicago’s Archdiocesan schools, said he’s “enormously excited” about the agreement and sees it as a new chapter in the Archdiocese’s 30-plus-year partnership with the Catholic nonprofit Big Shoulders Fund. The charity is set to spend $47.5 million on the schools’ operating costs over the next 10 years, with the Archdiocese contributing an additional $44.9 million.

”Big Shoulders is not going to be writing a substantial check to the Archdiocese every year,” Rigg said. “Rather, they’ll be working with the schools to cover a substantial portion of their ongoing operational budget.”

Though Big Shoulders will be financing a large part of the schools’ operations and will have a “central role” in running the schools, Rigg said the schools are still owned by the Archdiocese, and staff will still be employed by the Archdiocese.

“I have a lot of confidence in the expertise and the knowledge of the Big Shoulders team,” Rigg said.

Big Shoulders Fund was founded in 1986 as a scholarship program to support high-need Catholic schools in Chicago and today works with 75 schools, all but one of which are in the city. The 30 receiving the cash infusion are schools with which Big Shoulders already has a partnership.

But for the past several years, the nonprofit has expanded its work in the schools beyond just providing scholarships, said Josh Hale, president and CEO of Big Shoulders Fund.

The “historic agreement” between the Big Shoulders Fund and the Archdiocese grants the organization authority over teacher development, allows it to create educational curricula and grants them access to each school’s finances, officials said.

Big Shoulders will implement math, literacy and science programs in each of the 30 schools and work jointly with principals as they oversee operations. Hale said the organization has a team of former teachers, principals and curricula creators that are working inside of each school.

“We want those schools to be strong and viable for the community which is why we take this holistic approach,” Hale said. “We have a regular presence in our schools.”

Rigg said all 30 schools, which are primarily on the South and West sides of the city and serve a combined 5,600 students, have inherent budgetary struggles because they serve high-poverty populations that can’t always afford tuition, the primary source of revenue for any Catholic school. He added that broader population declines in Illinois and Chicago have hurt Catholic schools just as they have public districts, and the Archdiocese will work to attract new students.

Principal Philip Bazile at Augustus Tolton Academy in Park Manor said the new funding will help with the school’s overhead costs, including teacher salaries, building maintenance and after-school activities.

“This means survival for our school, really,” Bazile said. “Everything will be funded — from school supplies to our programming — by Big Shoulders.”

It isn’t clear yet how much will be allocated directly to Augustus Tolton Academy or other schools, but Bazile said it’s a “substantial amount of money.”

Epiphany Catholic School Principal Scott Ernst said the strings attached to the money are a huge benefit for the schools.

“It really is wonderful news that enhances what we are doing and gives us even more security to stay strong for another 100 years,” Ernst said. “Our teachers will have excellent professional development and we have the financing to back all of our programs.”

The five schools that are closing at the end of this school year weren’t saved in part because they don’t have a relationship with Big Shoulders, Rigg said. Four are in the suburbs, where Big Shoulders doesn’t operate, and the one in Chicago doesn’t serve a high-poverty neighborhood.

But that explanation was of little comfort to those upset by the decision to close the schools, including Nikko Popp, a 2009 graduate of St Jane de Chantal.

“It’s a slap in the face that they found funding for those schools but not ours,” said Popp, 25, who now lives in Arizona.

Asked why the Archdiocese didn’t separately earmark money for those schools but gave $45 million to these 30, Rigg said “sometimes we do have to make difficult decisions about the future when there are significant financial challenges.”

He said schools that are struggling financially and going through enrollment declines are given fundraising goals, and when those goals aren’t met, there’s little choice left.

Rigg denied, however, that the schools’ financial struggles were tied to the Archdiocese’s significant sex abuse-related debt.

“The Cardinal has pledged not to use the operating funds of the Archdiocese for sex abuse settlements,” Rigg said. “As a whole, the settlements are not taking away money from the school system.”

Here are the schools and their neighborhoods: