In 1996, Blagojevich surrendered his seat in the state house to campaign in Illinois's 5th congressional district. The district had long been represented by the powerful Democrat, Daniel Rostenkowski, who served as chairman of the House Ways and Means Committee. Rostenkowski was defeated for re-election in 1994 after pleading guilty to mail fraud and had been succeeded by Republican Michael Patrick Flanagan. Blagojevich soundly defeated Flanagan, with support from his father-in-law. He was elected two more times, taking 74% against a nominal Republican challenger in 1998 and having only a Libertarian opponent during 2000. He was not known as a particularly active congressman. In the late 1990s he traveled with Jesse Jackson, Jr. to Belgrade in the Federal Republic of Yugoslavia to negotiate with President Slobodan Milošević for the release of American prisoners of war.
On October 10, 2002, Rod Blagojevich was among the 81 House Democrats who voted in favor of authorizing the invasion of Iraq. He was the only Democrat from Illinois to vote in favor of the Iraq War.