On January 25, 2007, Johnson responded to U.S. PresidentGeorge W. Bush's State of the Union address by criticizing the war in Iraq, saying "This war has proven to be one of the gravest missteps in the recent history of our country. It is time for President Bush to face the music and respond to the urgent demands of a frustrated country."[10]

On February 8, 2007, Johnson introduced his first bill: a resolution requesting that the Secretary of Defense Robert Gates take U.S. troops off of street patrol duty in Iraq. "There is no military solution for the civil war in Iraq," said Johnson, "It is time for Iraqi troops, who have been trained, to assume responsibility for patrolling their own streets. Clearly, deploying our troops this way has only escalated the number of U.S. casualties, and this must stop".[11] According to the Atlanta Journal-Constitution, Johnson's resolution was "interesting in that it goes beyond broad directives and proposes something very specific".[12]

On March 23, 2007, Johnson voted to pass H.R. 1591, the "U.S. Troop Readiness, Veterans' Care, Katrina Recovery, and Iraq Accountability Appropriations Act, 2007". Amongst many other provisions, this bill provided $124 billion for military operations in Iraq and Afghanistan and required that President Bush withdraw American forces from Iraq by mid-2008; it additionally prohibited the use of funds offered under the act to deploy any troops to Iraq unless the military has certified to congressional appropriators in advance that the military unit is fully mission-capable (while authorizing the president to waive the prohibition and deployment limits on a unit-by-unit basis for reasons of national security). The proposed bill also set requirements for Department of Homeland Security contracts, subcontracts and task orders, and required that each federal agency that had awarded at least $1 billion worth of contracts in the preceding fiscal year develop and implement a plan to minimize the use of no-bid and cost-reimbursement contracts; provided funds for disaster relief and recovery related to hurricanes Katrina and Rita, for influenza pandemic response programs, for livestock disaster assistance, and made appropriations to bolster Medicare and Medicaid; it amended fair labor laws to phase-in an increase of the federal minimum wage to $7.25 per hour and applied these wage requirements to the Commonwealth of the Northern Mariana Islands and to American Samoa; addressed several tax issues by including tax breaks for small businesses, making certain dependents ineligible for the lowest capital gains rate, and lengthening the period of failure to notify a taxpayer of liability before interest and certain penalties must be suspended. The measure also increased the amount of any required installment of estimated tax otherwise due in 2012 from a corporation with assets of $1 billion or more.[13]
Johnson attracted attention by blogging about his decision to vote for the bill.[14] H.R. 1591 passed the House on 23 March 2007, and the Senate on 26 April, but President Bush, citing[15] the Iraqi withdrawal timeline incorporated among the many particulars as being unacceptable, vetoed the bill on 1 May 2007; Congress tried to override the veto the next day, but proved unable to do so.[16]

On May 24, 2007, Johnson voted to cut funding for the Iraq War unless provisions included binding requirements upon the Iraqi government and provisions were additionally made for the redeployment of American armed forces from Iraq.[17]

Johnson apologized on Twitter for his "poor choice of words", but added that Israeli settlements were undermining the two-state solution. In a statement his office made to The Atlanta Journal-Constitution he clarified that his termite metaphor referred to the corrosive process of settlement policies, "not the people."[24][25][26][27]J Street responded to Johnson's clarification by stating there should be no place for slurs, but, in their view the Congressman was speaking of the settlement enterprise not of individuals. Media coverage, they added, ought focus on opposition to settlement growth rather than on the misrepresentations by an irresponsible media outlet.[28]

Representative Johnson has supported legislation aimed at strengthening the U.S. civil justice system. In March 2016, Rep. Johnson and Representative John Conyers introduced legislation to protect consumers access to civil courts, titled the "Restoring Statutory Rights Act." This legislation would "ensure that the state, federal, and constitutional rights of Americans are enforceable" and consumers aren't forced into secretive private arbitration hearings.[29]

In 2007, Johnson's H.Con.Res.80, a resolution calling for peaceful resolution to the Ugandan civil war between the Government of Uganda and the Lord's Resistance Army, unanimously passed the House and Senate. Johnson's first successful piece of legislation, it was jointly introduced in the Senate by Democratic Senator Russ Feingold and Republican Senator Sam Brownback.

During a House Armed Services Committee hearing on March 25, 2010[31] concerning the U.S. military installation on the island of Guam, Johnson said to Admiral Robert F. Willard, Commander of U.S. Pacific Command, "My fear is that the whole island will become so overly populated that it will tip over and capsize", to which Admiral Willard replied, "We don't anticipate that."[32][33][34] Johnson later said that he was using a facetious metaphor.[35]

In 2014, Johnson was named the 18th most effective Democrat in the 112th Congress [out of 204 Democratic members] according to a new study by Vanderbilt University and the University of Virginia (UVA).[36] He was also ranked higher than any of his Republican colleagues from Georgia. The study judged effectiveness by looking at a lawmaker's "proven ability to advance a member's agenda items through the legislative process and into law." The scorecard looked at the number of bills a member introduced or sponsored; the significance of the bills; and how far each made it in the legislative process.[37]

In 2006, Johnson challenged Congresswoman Cynthia McKinney in the Democratic primary for the 4th District—the real contest in this heavily Democratic, black-majority district. He forced McKinney into a runoff by holding her under 50% in the July 18, 2006 Democratic primary: McKinney got 47.1% of the vote; Johnson 44.4%, and a third candidate got 8.5%.[39]

In the runoff of August 8, 2006, although there were about 8,000 more voters, McKinney got about the same number of votes as in the July primary. Johnson won with 41,178 votes (59%); McKinney got 28,832 (41%).[40]

On October 6, 2006, Congressional Quarterly's "On Their Way," which features promising candidates soon-to-arrive in Washington, featured Johnson.[41]

In November 2006, he trounced the Republican candidate, Catherine Davis, with 76% of the vote—one of the largest percentages for a Democrat in a contested election, and the largest in the history of the district. However, he had effectively clinched a seat in Congress with his victory in the primary. The 4th is one of the most Democratic districts in the South; with a Cook Partisan Voting Index of D+22 at the time of the election, it was the second-most Democratic district in Georgia (only the neighboring 5th is more Democratic).

Johnson made aggressive use of the internet to court supporters and attract national attention to his primary challenge against McKinney. The National Journal wrote that of all Congressional candidates nationwide in 2006, "Johnson had the most unique blog strategy by far."[42] The National Journal ranked Johnson's use of the internet to defeat McKinney—and the broader trend of challengers using the blogosphere to challenge entrenched incumbents—as the third most significant blog-related story of 2006.[43] Johnson was the first Congressional candidate invited to blog[citation needed] for The Hill's Congress Blog, typically reserved for Members of Congress.[44] "I'm tremendously excited about the opportunity to use this unique medium to strengthen democracy by increasing open interaction between constituents and candidates," Johnson wrote. "I hope to provide you with an inside view of this hotly-contested, high stakes runoff."

Johnson won reelection over the Republican candidate, business owner Liz Carter, gaining 131,760 of 176,467 votes, or 74.67% of the total.
Carter, who is white, made headlines during the campaign by maintaining that she had been initially barred from appearing at a candidate forum hosted by Newsmakers Journal due to her race, an assertion subsequently denied in a statement by the forum's organizers.[46]

Johnson is married to attorney Mereda Davis Johnson; they have two children.[47]

In December 2009, Johnson revealed that he had been battling Hepatitis C (HCV) for over a decade, which resulted in slow speech and a tendency to regularly get "lost in thought in the middle of a discussion".[48] Johnson said that he learned he had the disease in 1998 but did not know how he contracted it. HCV-induced liver dysfunction often leads to hepatic encephalopathy, a cause of confusion. Symptoms are often reversible with treatment.[49] The disease damaged his liver and led to thyroid problems.[48] He was treated with a combination of ribavirin and interferon at Walter Reed Army Medical Center.[48] In February 2010, Johnson successfully completed an experimental treatment for Hepatitis C, which resulted in restored mental acuity, weight gain and increased energy.[50]