Koonz first came to fame in 1969 with a dissertation on Walther Rathenau. She was awarded a PhD from Rutgers University in 1970. She has taught at the College of the Holy Cross in Worcester, Massachusetts and at Duke University.

Koonz is best known for documenting the appeal of Nazism to German women, and that German women played an enthusiastic role in supporting the Nazi regime. Koonz has established that the leaders of German feminist groups were happy to go along with Gleichschaltung that coerced Germans into following Nazi policy. Koonz has noted that female supporters of the Nazis accepted the Nazi division of the sexes into a public sphere for men and a private sphere for women. Koonz has claimed that women involved in resistance activities were more likely to escape notice owing to the 'masculine' values of the Third Reich. Another notable claim made by Koonz is that women who most successfully asserted themselves in the Third Reich were also the women who violated the norms of civilized society such as Ilse Koch. Koonz maintains that only women who were opposed to Nazism 100% can be considered to be a resistance; those women who protested against sterilization and the Action T4 program, but who did not protest the deportation of Jews to death camps are not considered by Koonz to be part of the resistance. Koonz's views have often had her pitted against Gisela Bock in battle some have referred to as the Historikerinnenstreit (Women Historians' Dispute).

Koonz is one of the "Group of 88" professors who, in the wake of the Lacrosse players scandal, signed a controversial letter thanking protesters for "making a collective noise" on "what happened to this young woman." The letter has been widely criticized as a prejudgment since no sexual assault occurred. All charges against the players were eventually dismissed and the District Attorney who prosecuted the case, Michael Nifong, was disbarred and jailed.