Gaffney is a 1975 graduate of the Edmund A. Walsh School of Foreign Service of Georgetown University.[citation needed] He holds a graduate degree from the Johns Hopkins University's Paul H. Nitze School of Advanced International Studies.

Gaffney began his public service career in the 1970s, working as an aide in the office of Democratic Senator Henry M. Jackson, under Richard Perle. From August 1983 until November 1987, Gaffney held the position of Deputy Assistant Secretary of Defense for Nuclear Forces and Arms Control Policy in the Reagan Administration, again serving under Perle. In April 1987, Gaffney was nominated to the position of US Assistant Secretary of Defense for International Security Policy. He served as the acting Assistant Secretary for seven months, though his confirmation was ultimately blocked by the United States Senate.

In 1988, Gaffney established the Center for Security Policy (CSP), a conservative national security and defense policy organization. The CSP is subsidized by donors supportive of conservative causes, including the Sarah Mellon Scaife Foundation, the Shelby Cullom Davis Foundation and the William H. Donner Foundation.

Gaffney appeared on FahrenHYPE 9/11, the conservative documentary that was intended as a rebuttal to Michael Moore's liberal film Fahrenheit 9/11. He is also a regular guest on MSNBC's "Hardball with Chris Matthews" show.

Gaffney was an executive producer for the documentary Islam vs. Islamists: Voices from the Muslim Center. The documentary was created to air as part of the America at a Crossroads series on PBS, but it has not been shown.

Gaffney is the lead author of War Footing (Naval Institute Press, 2005), a collection of essays that "offer ten specific steps that Americans, as individuals and as communities, can take to ensure their way of life and safety and the future well-being of their children and grandchildren."

He is a founding member of the Set America Free Coalition, dedicated to reducing dependence on foreign oil, as well as of the current iteration of the Committee on the Present Danger.

In 2010 Gaffney has begun tweeting explosive accusations followed by links to his podcast. However, evidence to support the provocative twitter messages is not typically found by following the link. Examples in July 2010 include the accusation that Supreme Court nominee Elena Kagan advocated for Sharia law, and that Hezbollah is "training on the US/Mexico border."

In November 1992, Gaffney's Center for Security Policy organization released a report detailing voter fraud in Angola's presidential election. Election officials stopped registering voters 40 days before the election. Polling stations had identical voting results. The MPLA retained a monopoly on television election-coverage. CSP also found widespread vote buying by the MPLA, the discarding of as many as 25% of casted ballots, and electricity blackouts during voter counting. United Nations special envoy Margaret Anstee said she "had never witnessed a more unfair election, even in Latin America."

Along with a number of figures who later assumed leading positions in the George W. Bush administration, Gaffney was one of 25 signatories of the June 3, 1997 "Statement of Principles" from the Project for the New American Century, an educational and political advocacy organization whose stated goal was "to promote American global leadership."