Milbank covered the 2000 US Presidential election and the 2004 US Presidential election. He also covered US President George W. Bush's first term in office. After Bush won the 2000 election, Karl Rove asked the Washington Post not to assign Milbank to cover White House news. In 2001, a pool report penned by Milbank which covered a Bush visit to the US Capitol generated controversy within conservative circles. According to Milbank, the nickname given to him by the president is "not printable in a family publication."
Milbank writes "Washington Sketch" for the Post, an observational column about political theater in the White House, Congress, and elsewhere in the capital. Before coming to the Post as a political writer in 2000, he covered the Clinton White House for The New Republic and Congress for The Wall Street Journal.
Milbank was criticized for a July 30, 2008 article in which, in part by using snippets of quotations, he portrayed Barack Obama as being presumptuous. A few days later MSNBC's Keith Olbermann stated that Milbank would not be allowed back onto his show, which Milbank had appeared on since 2004, until Milbank submitted "a correction or an explanation."  However, Milbank had apparently already left Olbermann's show for another show on CNN. Milbank stated that he has been dissatisfied since he was criticized by Olbermann's staff over making a positive comment about Charlie Black, a McCain senior advisor, and as a result had already been negotiating with CNN.
Milbank and Chris Cillizza appeared in a series of humor videos called "Mouthpiece Theater" which appeared on the Washington Post's website. An outcry followed a video in which, during a discussion of the White House "Beer Summit", they chose new brands for a number of people, including "Mad Bitch Beer" for Hillary Clinton. Both men apologized for the video and the series was canceled.