During the 1980s Kinzer covered revolution and social upheaval in Central America, as well as published his first book, Bitter Fruit, about military coups and destabilization in Guatemala during the 1950s. In 1990, the New York Times promoted Kinzer to bureau chief of its Berlin bureau, from which he covered the growth of Eastern and Central Europe as they emerged from Soviet rule. Kinzer was the New York Times chief in the newly established bureau in Istanbul (Turkey) from 1996 to 2000.
Upon returning to the United States, Kinzer became the newspaper's culture correspondent, based in Chicago, as well as teaching at Northwestern University. Kinzer then took up residence in Boston and began teaching journalism and United States foreign policy at Boston University. He has written several non-fiction books about Turkey, Central America, Iran, the US overthrow of foreign governments from the late 19th century to the present, as well as Rwanda's recovery from genocide.
Kinzer also contributes columns to the New York Review of Books, The Guardian, and the Boston Globe. He is a Senior Fellow in International and Public Affairs at the Watson Institute for International and Public Affairs at Brown University.
Kinzer's reporting on Central America was criticized by Edward S. Herman and Noam Chomsky in their 1988 book Manufacturing Consent, which cited Edgar Chamorro ("selected by the CIA as press spokesman for the contras") in his interview by Fairness and Accuracy in Reporting describing Kinzer as:
"...like an errand boy, building up those stories that fit in with Reagan's agenda - one day it's the church, the next day it's the Miskitos, then the private sector. In the last two weeks I've seen eight articles by Kinzer that say exactly what the White House wants. Kinzer always raises questions about Sandinista intentions, whether they're truly democratic, and so on. When you analyse his articles you see he's just responding what the White House is saying."
Chomsky later expanded on this in an interview published in the 2002 collection Understanding Power:
Look, one of the things that Edward Herman and I did in Manufacturing Consent was to just look at the sources that reporters go to. In a part that I wrote, I happened to be discussing Central America, so I went through fifty articles by Stephen Kinzer of the New York Times beginning in October 1987, and just asked: whose opinions did he try to get? Well, it turns out that in fifty articles he did not talk to one person in Nicaragua who was pro-Sandinista. Now, there's got to be somebody -- you know, Ortega's mother, somebody's got to be pro-Sandinista. Nope, in fact, everybody he quotes is anti-Sandinista. [Daniel Ortega was the Sandinista President.] Well, there are polls, which the Times won't report, and they show that all of the opposition parties in Nicaragua combined had the support of only 9 percent of the population. But they have 100 percent of Stephen Kinzer - everyone he's found supports the opposition parties, 9 percent of the population. That's in fifty articles.
Kinzer has since that time criticized what he regards as an interventionist foreign policy of the United States toward Latin America and more recently the Middle East. In Overthrow: America's Century of Regime Change From Hawaii to Iraq, published in 2006, Kinzer critiqued U.S. foreign policy as overly interventionist. In a 2010 interview with Imagineer Magazine, he stated:
The effects of U.S. intervention in Latin America have been overwhelming negative. They have had the effect of reinforcing brutal and unjust social systems and crushing people who are fighting for what we would actually call 'American values.' In many cases, if you take Chile, Guatemala, or Honduras for examples, we actually overthrew governments that had principles similar to ours and replaced those democratic, quasi-democratic, or nationalist leaders with people who detest everything the United States stands for.
In his 2008 book A Thousand Hills: Rwanda's Rebirth and the Man who Dreamed It, Kinzer credits President Paul Kagame for what he describes as the peace, development, and stability in Rwanda in the years after the Rwandan genocide, and criticizes the leaders of Rwanda before the genocide, such as Juvenal Habyarimana.