On December 7, 1863, when the Thirty-Eighth Congress convened, the 31-year-old James A. Garfield was the second-youngest congressman in attendance. Garfield received an appointment to the military affairs committee and an appointment to a special committee investigating the expansion of the railroad system, but the most controversial measures of his early congressional career were related to the reconstruction of the American South. The tide had turned against the Confederacy with Union victories at Gettysburg and Vicksburg, and it appeared to be only a matter of time before the South could rejoin the Union. In 1864, Congress voted to establish a military government in each Confederate state until a majority of the white men in that state had taken an oath of allegiance. The following year, as the war dragged to a close, Garfield and the other congressmen debated a constitutional amendment that would outlaw slavery. On January 31, 1865, the amendment passed and became law by the end of that same year.

Garfield was reelected in 1864 and transferred to the Ways and Means committee, where he began to use the fiscal knowledge he had acquired over the years. He helped guide through the Revenue Law of 1866, which completely revamped the nation's tax system. The national debt had exploded from thirty million dollars before the war to over two billion at the end, and Garfield worked with his old Ohio friend Salmon P. Chase to lower the burden. As treasury secretary, Chase had introduced a national currency, but the value of the new money fluctuated greatly during the post-war period. In 1868, Garfield introduced legislation to set the value of the money and even out the fluctuations.

On March 6, 1866, Garfield argued the first legal case of his career–in front of the United States Supreme Court. In Ex Parte Milligan, one of the most famous cases arising out of the suspension of habeas corpus by President Abraham Lincoln, three men had been convicted of treason by the Indiana military commander and sentenced to hang. The accused argued, however, that the suspension was invalid, as was their conviction. Garfield argued, "Hang them if guilty, but hang them according to law; if you hang them otherwise, you commit murder." Garfield won the case and soon became in great demand as a lawyer.

In the Fortieth Congress, which convened in 1867, Garfield returned to the military affairs committee and made the introductory remarks at the dedication of Arlington National Cemetery the following year. In 1869, Garfield chaired a special committee on the 1870 census and won a coveted appointment to the House rules committee. However, Harding's most significant contribution was his dedication to tying paper money to gold, making a supporter of what was then called "hard money" supporter. With the election of Union general Ulysses S. Grant as president, Garfield found a loyal ally in his banking measures. From 1871 to 1875, Garfield served as chair of the appropriations committee, Congress's most powerful post, short of speaker. Garfield also oversaw the decreasing of the national debt and worked to ensure sound fiscal policies throughout government.

At the time, a growing issue in the United States was the issue of civil service reform. The federal government was suffering under the spoils system, wherein politicians rewarded their supporters with federal jobs. President Grant had been besieged by office seekers when he assumed his office and had established the first civil service commission to try and establish some kind of order. As chair of the appropriations committee, Garfield ensured the commission's financial survival. In 1873, however, Garfield drew criticism for including a salary increase for legislators and the president during last-minute negotiations in the House.

During his time in Congress, Garfield was tied to two scandals that tarnished his record. One scandal alleged that Garfield had accepted a bribe to delay a congressional investigation of Credit Mobilier Company, which had illegally profited off of government contracts. The other scandal involved accepting fees from a paving company trying to obtain a contract. In neither case was Garfield ever proven guilty.

The Democrats took control of the House in the 1874 elections amid a national sense of frustration about corruption in government. Garfield told friends he would not seek reelection, but later changed his mind.