Boston nonprofit Be The Change said recently that Kevin Jennings, the U.S. Department of Education’s assistant deputy secretary for safe and drug-free schools, will take over its organization in late July.

Mr. Jennings’ departure, which the Education Department said will be next week, comes a little less than two years after his somewhat controversial appointment.

Mr. Jennings began his career in education as a teacher in Rhode Island. He founded the Gay, Lesbian and Straight Education Network, a group that connects lesbian, gay, bisexual, transgender, and straight teachers, parents, students, and community members to work on ending bias and discrimination in schools.

A few years later, he was appointed co-chairman of a commission in Massachusetts focusing on gay and lesbian youth. The group led the fight that made Massachusetts the first state to outlaw discrimination against public school students on the basis of sexual orientation.

A few months after Mr. Jennings was named to the federal Education Department post, some conservative members of Congress called for his removal, saying Mr. Jennings, who is openly gay, “has played an integral role in promoting homosexuality and pushing a pro-homosexual agenda in America’s schools—an agenda that runs counter to the values that many parents desire to instill in their children.”

As assistant secretary, Mr. Jennings has become known for putting a spotlight on bullying. In October, the Education Department’s civil rights office issued a letter outlining schools’ roles in cases of bullying, stating “A school is responsible for addressing harassment incidents about which it knows or reasonably should have known.” In March, Mr. Jennings’ anti-bullying efforts culminated in conference at the White House addressing all forms of bullying.