The deputy superintendent of Atlanta Public Schools is leaving to lead the Boys & Girls Clubs of Metro Atlanta.

David Jernigan was hired in 2014 by Superintendent Meria Carstarphen to be her second-in-command. He oversees academic and student programs for the 52,000-student district and had previously worked as the executive director of the charter school network KIPP Metro Atlanta.

The Boys & Girls Clubs announced Tuesday it has hired Jernigan as its new president and chief executive officer. He will leave his APS post April 13 and begin his new job May 4.

In an email to APS administrators, Jernigan described his six years with the district as “some of the most fulfilling” of his life.

“I will be forever grateful to Dr. Carstarphen for taking a chance on me and for entrusting me with such an incredible to opportunity to serve…,” he wrote.

Jernigan went on to add: “Some of my most formative years as a child were spent at my local Boys & Girls Club in North Carolina, so I’ve seen firsthand the impact of Boys & Girls Clubs and truly believe the organization has the power to change lives and lift communities. I can’t imagine a better organization with which to begin my next chapter.”

Jernigan's departure from APS is the first big administrative change since the school board announced in September that it would not extend Carstarphen's contract. Carstarphen came to APS in 2014.

In a letter to colleagues, Carstarphen praised his work on behalf of APS and students.

“For the last six years, David has been my trusted right-hand, best thought partner and committed leader to ensure we stayed focused on our true north: the students of Atlanta Public Schools,” she wrote.

At APS, Jernigan supervised the work of associate superintendents, student programs and services, federal programs and the district’s charter school office.

The Boys & Girls Clubs of Metro Atlanta run more than 20 clubs in 10 metro counties that serve about 2,800 children and teens.

In a news release, the organization said more than 200 people applied for the president position, with Jernigan selected after an “extensive search.”