After his clerkship, Rosenstein joined the United States Department of Justice through the Attorney General's Honors Program.
From 1990 to 1993, he prosecuted public corruption cases as a trial attorney with the Public Integrity Section of the Criminal Division, the latter of which was led by then Assistant Attorney General Robert Mueller.

During the Clinton Administration, Rosenstein served as Counsel to Deputy Attorney General Philip B. Heymann (1993–1994) and Special Assistant to Criminal Division Assistant Attorney General Jo Ann Harris (1994–1995).
Rosenstein then worked in the United States Office of the Independent Counsel under Ken Starr on the Whitewater investigation into President Bill Clinton.
As an Associate Independent Counsel from 1995 to 1997, he was co-counsel in the trial of three defendants who were convicted of fraud, and he supervised the investigation that found no basis for criminal prosecution of White House officials who had obtained FBI background reports.

United States Attorney Lynne A. Battaglia hired Rosenstein as an Assistant U.S. Attorney for the District of Maryland in 1997.

From 2001 to 2005, Rosenstein served as Principal Deputy Assistant Attorney General for the Tax Division of the United States Department of Justice.
He coordinated the tax enforcement activities of the Tax Division, the U.S. Attorneys' Offices and the IRS, and he supervised 90 attorneys and 30 support employees.
He oversaw civil litigation and served as the acting head of the Tax Division when Assistant Attorney General Eileen J. O'Connor was unavailable, and he personally briefed and argued civil appeals in several federal appellate courts.
After his clerkship, Rosenstein joined the United States Department of Justice through the Attorney General's Honors Program. From 1990 to 1993, he prosecuted public corruption cases as a trial attorney with the Public Integrity Section of the Criminal Division, the latter of which was led by then Assistant Attorney General Robert Mueller.
During the Clinton Administration, Rosenstein served as Counsel to Deputy Attorney General Philip B. Heymann (1993–1994) and Special Assistant to Criminal Division Assistant Attorney General Jo Ann Harris (1994–1995). Rosenstein then worked in the United States Office of the Independent Counsel under Ken Starr on the Whitewater investigation into President Bill Clinton. As an Associate Independent Counsel from 1995 to 1997, he was co-counsel in the trial of three defendants who were convicted of fraud, and he supervised the investigation that found no basis for criminal prosecution of White House officials who had obtained FBI background reports.
United States Attorney Lynne A. Battaglia hired Rosenstein as an Assistant U.S. Attorney for the District of Maryland in 1997.
From 2001 to 2005, Rosenstein served as Principal Deputy Assistant Attorney General for the Tax Division of the United States Department of Justice. He coordinated the tax enforcement activities of the Tax Division, the U.S. Attorneys' Offices and the IRS, and he supervised 90 attorneys and 30 support employees. He oversaw civil litigation and served as the acting head of the Tax Division when Assistant Attorney General Eileen J. O'Connor was unavailable, and he personally briefed and argued civil appeals in several federal appellate courts.
Rod Rosenstein