The schools are clustered in the northeast San Fernando Valley, East Los Angeles and South Los Angeles.
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The claim follows passage of Proposition 30 and state legislation which designated funds for children most at risk.
RELATED: Lawsuit settlement documents, including list of schools
The ACLU, Community Coalition and Public Advocates alleged that LAUSD's accounting failed to pass along the funds to the targeted groups.
"There was a flaw in the way they were calculating this funding and we were aggressive about letting them know, fix it fix it," said ACLU Education Equity director Sylvia Torres-Guillen.
LAUSD said it is pleased with the settlement and in a statement described the accounting process as complicated.
"The underlying litigation between the parties involved varying interpretations of a very complex statutory framework," stated LAUSD General Counsel David Holmquist.
The funds will provide new services for English-language learners, low-income students and youth in foster care who need support to catch up.
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"When children get to school they are already behind because they didn't get the right academic supports from middle school," said Aurea Montes-Rodriguez of the Community Coalition.
The students often arrive at school stressed out by gun violence in neighborhoods surrounding their school and need trained counselors which have been absent.
"We know these funds are going to have an immediate positive impact on the students, the schools and the community," Montes-Rodriguez said.
The funds will be disbursed over the next three years.
The schools must present plans for how they will use the funds which must be approved by the LAUSD superintendent.