Morgenson graduated in 1976 from Saint Olaf College in Northfield, Minnesota with a B.A. degree in English and history. She went to work as an assistant editor with Vogue magazine, eventually becoming a writer and financial columnist. In 1981 she co-authored the book The Woman's Guide to the Stock Market and that same year joined the Wall Street stockbrokerage, Dean Witter Reynolds where she remained until January 1984. She returned to writing on financial matters at Money magazine and in late 1986 accepted an offer from Forbes magazine to work as an editor and an investigative business writer. In mid 1993, she left Forbes magazine to become the executive editor at Worth magazine but in September 1995 took on the job of press secretary for the Presidential election campaign of Steve Forbes following which she was appointed assistant managing editor at Forbes magazine.

She is married, has a son and lives in New York City.

In May 1998 Gretchen Morgenson became the assistant business and financial editor at the New York Times. She has written about the conflicts of interests between financial analysts and their employers who generate income money from the companies that the analysts assess.

Beginning in 2005, Morgenson has been focusing on executive compensation packages being paid by American companies that she asserts has reached levels far in excess of what can be justified to shareholders.

In 2006, Morgenson broke a story about a Wall Street analyst (Matthew Murray) who was fired shortly after he reported emails to Congress concerning potential violations of SEC regulation AC by the investment bank (Rodman & Renshaw) that he worked for at the time. The emails allegedly documented that the investment bank wouldn't let the analyst lower his rating, or have his name removed from coverage, of an investment banking client. A subsequent article by Morgenson highlighted a letter she obtained from the Senate Finance Committee in which Senator Grassley stated that the investment bank's Chairman (General Wesley Clark) had acknowledged to his staff that the analyst had been fired from the investment bank as a result of reporting the emails to Congress. A blog called ResearchIndependence.org [1] has links to the Morgenson articles and other documents related to the incident.

In 2009, The Nation called her "The Most Important Financial Journalist of Her Generation".She has appeared on Bill Moyers Journal, and Charlie Rose.

Morgenson's articles have been described by Calculated Risk, a popular financial and economics blog, as "a noxious mixture of fact and hype, information and innuendo." Calculated Risk further notes that several of Morgenson's stories were broken not by Morgenson but rather on financial blogs, and that this fact was not noted by Morgenson in her articles. Other bloggers have questioned whether Morgenson's articles would be better categorized as editorials instead as news stories.