Brown was elected to the Florida House of Representatives in 1982. She served five terms, gaining wide recognition in the Jacksonville area, and served as a delegate to the 1988 Democratic National Convention. After the 1990 census, the Florida legislature carved out a new Third Congressional District in the northern part of the state. This district was designed to enclose an African-American majority within its boundaries. A horseshoe-shaped district touching on predominantly African-American neighborhoods in Jacksonville, Gainesville, Orlando, and Ocala, the Third District seemed likely to send Florida's first African-American to Congress since Reconstruction, and Brown decided to run.
Brown faced several candidates in the 1992 Democratic primary, but the strongest opponent to emerge was a white talk radio host from Jacksonville named Andy Johnson. Johnson, according to the Almanac of American Politics, called himself "the blackest candidate in the race." Brown defeated Johnson in the primary and in a two-candidate runoff, and went on to win the general election in November of 1992. In 1995, the boundaries of the Third District were struck down by the Supreme Court due to their irregular shape, and the percentage of African American residents of the district declined to about 47 percent. One of the main instigators of the lawsuit that led to the redistricting was Brown's old political rival, Andy Johnson. Brown railed against the change, complaining that "[t]he Bubba I beat [Johnson] couldn't win at the ballot box [so] he took it to court," as she was quoted as saying in the New Republic. Brown won in her new white majority district in 1996.
Brown has enjoyed some of her strongest support from religious leaders. She also receives PAC money from organized labor and the sugar industry.
A few weeks after becoming a member of the U.S. House in 1993, the Federal Elections Commission began investigating her. Her former campaign treasurer quit and said Brown had neglected to take action against an aide who had committed forgery, forging the treasurer's signature on her financial documents. The staffer alleged to have forged the treasurer's signature stayed with Brown and as of 1998 was her chief of staff. In 1996, there was another investigation concerning charges that Brown improperly received and spent a $10,000 check from a secret account used for money laundering by National Baptist Convention leader Henry Lyons. Brown admitted receiving the check but denied she had used the money improperly. She was accused of not reporting the check or reporting who she received the money from. Brown said that she had taken the check and converted it into another check made out to Pameron Bus Tours to pay for transportation to a rally she organized in Tallahassee. She said that she didn't have to report the money because the rally was to protest the reorganization of her district lines, and she did not use it for herself. If the $10,000 gift had been reported, it would have exceeded the $1,000 individual donation limit.
Brown had had previous dealings with Lyons; in 1992, her campaign paid $5,000, allegedly for a computer, to a company owned by Lyons. The company had shut down six years earlier. Her office once arranged for Lyons to buy several airline tickets at the government discount rate. Under Congressional rules, only members of Congress and their staffers are allowed to take this rate.
On February 25, 2004 Brown referred to the George W. Bush administration as a "racist" "bunch of white men" in a meeting with senior State Department officials and members of Congress. Assistant Secretary of State Roger Noriega, a Mexican American, said that he deeply resented "being called a racist and branded a white man." Brown replied to Noriega and Cuban-American Representative Lincoln Diaz-Balart that "you all look alike to me". Brown later apologized for her statements, but still contends that President Bush's involvement in the 2004 Haiti Rebellion was racist.
In June 2007, Citizens for Ethics released a report reporting Brown's daughter Shantrel Brown-Fields as a congressional lobbyist; the organization maintains that Congressional relatives working as lobbyists for special interests are a conflict of interest for lawmakers. Brown-Fields is employed by Alcalde & Fayte, with clients including ITERA, Miami-Dade County Commission, and Edward Waters College. In 2006, Brown's campaign committee paid her daughter's husband, Tyree Fields, $5,500 for political consulting work. Rep. Brown has earmarked millions of dollars in federal funding for her daughter's client Edward Waters College.
City vehicles showed up, with a crew of inmates because the city uses low-risk inmates to do work, to sandbag the garage and front door after she was flooded with about a foot of water. Brown got angry with the reporter from Channel 4 doing the interview, demanding that the City of Jacksonville figure out how much it cost and she would "pay the bill" to silence any controversy. According to her neighbor, Joe Deloach, asked for the same help from the crew of inmates sandbagging Ms. Brown's property, but was denied and laughed at by the crew working on the project.
On the first day of early voting for the 2004 General Election, Brown, with several supporters, stood on the steps of the entrance of the Duval County Supervisor of Elections headquarters, an early voting site, and began passing out a "pseudo-ballot," directing people to vote for only Democratic candidates and Florida amendments that should pass. It was not until noon that Brown and her supporters moved to the mandatory fifty feet away from the entrance. Brown claimed her intention had been to increase awareness of early voting, and that she had not knowingly violated the fifty feet rule.
In July 2004 Brown was censured by the House of Representatives after she referred to the disputed 2000 presidential election in Florida as a "coup d'état". This comment came during floor debate over HR-4818, which would have provided for international monitoring of the 2004 U.S. presidential election.
Brown was one of the 31 representatives who voted against counting the electoral votes from Ohio in the United States presidential election, 2004. In 2006, she voted "no" on the Child Custody Protection Act, Public Expression of Religion Act, Electronic Surveillance Modernization Act, Military Commissions Act, and Private Property Rights Implementation Act of 2006. She voted "yes" on the SAFE Port Act. On September 29, 2008, Brown voted for the Emergency Economic Stabilization Act of 2008.