Secret Service Director Joseph Clancy announced his retirement Tuesday after two years at the helm of the agency.

In a message to employees, Mr. Clancy, 61, said his retirement will take effect in less than three weeks.

“I am announcing I will retire from the Secret Service effective March 4,” Mr. Clancy said. “As all of you know, President Trump and his administration have been very supportive of this agency and of me personally which makes this a very difficult decision.”

His departure means that Mr. Trump will now choose the person he wants to lead the protective service.

President Obama tapped Mr. Clancy as acting director in 2014 to lead the agency with more than 7,000 employees out of a series of scandals. After a long career at the agency serving on presidential protective details, Mr. Clancy had left the Secret Service in 2011 to become head of security for Comcast.

“My love for this agency has only complicated the decision further, but for personal reasons it is time,” he said. “I look forward to spending time with my family.”

House Judiciary Committee Chairman Bob Goodlatte, Virginia Republican, said Mr. Clancy “has served our nation honorably for decades by protecting several presidents, their families, and the White House complex from harm.”

“Under Director Clancy’s leadership, the Secret Service did a stellar job protecting presidential candidates during the 2016 election,” Mr. Goodlatte said. “He also helped restore professionalism at the agency after a series of security lapses and incidents of misconduct over the past few years.”

Mr. Obama asked Mr. Clancy to run the Service after Director Julia A. Pierson resigned in the wake of the agency’s failure in 2014 to stop a knife-wielding man from entering the White House after he climbed over a fence along Pennsylvania Avenue.

In 2012, eight agents were fired after the disclosure that they allegedly solicited prostitutes during an official trip to Colombia.

Sen. Patrick J. Leahy, Vermont Democrat and a member of the Senate Judiciary Committee, said Mr. Clancy “took over the United States Secret Service during an era of great challenges, and he has provided much needed leadership and stability during his tenure.”

“At a time when our nation is facing serious national security challenges, I hope the president appoints someone similarly qualified to lead the Secret Service,” Mr. Leahy said.

Mr. Trump repeatedly thanked the Secret Service for their professionalism and quick action during the campaign, such as when a man rushed the stage as Mr. Trump was speaking during a rally in Dayton, Ohio, in March 2016. Agents subdued the man, a 22-year-old college student who later pleaded guilty and was fined.

But Mr. Trump also used private security at campaign events, creating some friction with the Secret Service. And as president, Mr. Trump hired his former security director, Keith Schiller, to be his director of Oval Office operations.

A statement from the Secret Service said Mr. Clancy, who worked 30 years for the government, “was best known by Secret Service employees as a sincere and genuine leader, who walked the line to engage his people.”

“He understood the challenges faced by the frontline agents, officers and professional staff, and it was that understanding that guided his sound decisions,” the statement said. “While his focus remained on the mission, he strove to improve the quality of life challenges, which faced his people. His accomplishments in this endeavor included record increases in recruiting and hiring. His personal and soft-spoken style will be greatly missed as the agency continues its role to safeguard the “executive branch of government and the nation’s financial systems.”

“The Secret Service family is grateful for his extraordinary leadership, and wishes him all the best in his next chapter of his life,” the agency said.

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