David C. Banks, the chancellor of New York City’s public school system, said on Tuesday that he would resign from his post at the end of December.

Mr. Banks, who was the first major appointment of Mayor Eric Adams’s administration, announced his departure only a few weeks after federal agents seized his phone, and as the city government is embroiled in a wide-ranging corruption scandal that has led to the resignation of the police commissioner and the city’s top lawyer. The health commissioner also announced earlier this week that he would be leaving the administration by the end of the year.

That Mr. Banks, one of the mayor’s closest allies and friends, would leave the administration at its lowest moment — and the school system at midyear — demonstrates the depth of the crisis at City Hall. He has said since at least the mid-1990s that leading New York City’s school system, the nation’s largest, was the job he wanted more than any other.

The chancellor had his phone seized around dawn on Sept. 4, just before the first day of school, as part of an investigation that appears to be focused at least in part on a consulting firm run by his youngest brother.

Mr. Banks’s fiancée, Sheena Wright, the first deputy mayor, also had her phone seized when federal agents appeared at their door. And another brother, Philip B. Banks III, the deputy mayor for public safety, also had his phone taken by federal agents.

“I have always lived my life with integrity, every day,” Chancellor Banks said at a recent news conference, when asked about the searches.

In a statement on Tuesday, Mr. Adams thanked the chancellor, and said that the public school system had “transformed” in the three years that he had run it.

“On behalf of all New Yorkers, we thank Chancellor Banks for his service, and wish him well in his retirement at the end of the calendar year,” he added.

It was not immediately clear who would replace the chancellor.

This is a developing story and will be updated.

Jan Ransom contributed reporting.