Mayor Bill de Blasio and City Council Speaker Corey Johnson reached a three-year, $15 million deal with unions to boost the pay of early childhood educators working for nonprofits.

“We cannot have a system where certified teachers at community-based organizations start out earning thousands of dollars less than those doing the same job in public schools,” Johnson said Tuesday at a City Hall press conference announcing the agreement.

The deal with District Councils 37 and 1701 will be voted on by those unions’ members in the coming weeks and is expected to be approved, said DC 37 director Henry Garrido.

Garrido said there’s a 30 percent turnover rate for nonprofit early education workers compared to just 10 percent for their Department of Education counterparts because of the salary gap.

The deal will raise the pay of over 300 certified pre-K teachers by $17,000 to $20,000, depending on their education level, over the next three years — making their salaries commensurate with their DOE counterparts’. The increases start in the fall. By October 2021, teachers with a master’s degree will earn $68,652 and those with a bachelor’s degree will make $61,070.

Another 3,900 uncertified teachers and support staff will get a $1,800 bonus and a 2.75% percent wage increase by October 2020. Union members will also get reduced health care costs as part of the deal.

The agreement will be funded with $10 million from the city’s labor reserves plus an additional $5 million in new outlays by the fiscal year 2023.

Some 12,000 non-unionized employees, including those working for charter schools, Head Start programs and religious providers, are not part of the deal.

“Bill de Blasio brags to national voters that he’s Mr. Pre-K while not fully funding pre-K back home. Excluding charters and Head Starts from this deal shows Mayor de Blasio cares more about politics than kids,” said Jenny Sedlis, director of the advocacy group StudentsFirstNY.

De Blasio has made his free pre-K program that educates 70,000 kids a centerpiece of his long-shot presidential bid.

The mayor’s labor relations director, Renee Campion, said the agreement provides a “framework” to negotiate similar deals for workers who were left out of this one.