He was the director of the Eagleton Institute of Politics, where he also led the Miller Center for Community Protection and Resilience (CPR).

Following Governor Christine Todd Whitman's resignation the previous year to become head of the EPA, Farmer was one of four people to serve as acting governor for the one-year period between Whitman's resignation and Jim McGreevey's inauguration, along with three different senate presidents, Donald DiFrancesco, John O. Bennett, and Richard Codey.

As a result, the state had five different people serving as governor during a period of eight days: DiFrancesco, Farmer, Bennett, Codey, and McGreevey.

[6] Farmer subsequently acted as senior counsel to the 9/11 Commission, chaired by former New Jersey Governor Thomas Kean.

In his tenure, In conjunction with Rutgers Law Review, Farmer planned a multi-day symposium to address the many legal uncertainties in national security policies and practices following the September 11 terrorist attacks.

Two United States Supreme Court justices, Stephen Breyer and Samuel Alito, also have spoken at the law school.

On April 11, 2013, he was appointed as the senior vice president and general counsel at Rutgers University in New Brunswick, New Jersey.

On August 19, 2019, Farmer was appointed by Chancellor Christopher J. Molloy to succeed Ruth B. Mandel as the director of the Eagleton Institute of Politics at Rutgers University.