On April 4, 1861, the Kansas legislature elected Pomeroy to be one of Kansas's first federal senators. In 1863, during the Civil War, Pomeroy escorted Frederick Douglass to the War Department building to meet War Secretary Edwin Stanton. Afterwards, Douglass attended a meeting with President Abraham Lincoln. In 1864, Pomeroy was the chair of a committee supporting Secretary of the Treasury Salmon P. Chase for the Republican nomination for President of the United States over the incumbent, Abraham Lincoln. Pomeroy also spoke in support of Chase's candidacy in the Senate. The Pomeroy committee issued a confidential circular to leading Republicans in February 1864 attacking Lincoln, which had the unintended effect of galvanizing support for Lincoln and seriously damaging Chase's prospects.
During the Kansas senatorial election of 1873, it was alleged that Senator Pomeroy paid $7,000 to Mr. Alexander M. York, a Kansas state senator, to secure his vote for reelection to the Senate by the Kansas State Legislature. York publicly disclosed the alleged bribe was an attempt to pin a bribery charge against the senator. Pomeroy ultimately lost the election to John J. Ingalls. State Senator York was also one of the brothers of Dr. William York, one of the murder victims of the Bloody Benders Family. Pomeroy took to the Senate floor on February 10, 1873 to deny the allegations as a "conspiracy... for the purpose of accomplishing my defeat," and urged the creation of a special committee to investigate the allegations. The payment of the $7,000 was never disputed by witnesses, but instead of being a bribe it was described to the committee as a payment meant to be passed along to a second individual as seed money to start a national bank. The Special Committee on the Kansas Senatorial Election issued its report on March 3, 1873, which determined there was insufficient evidence to sustain the bribery charge, and instead was part of a "concerted plot" to defeat Senator Pomeroy. Senator Allen G. Thurman of Ohio disagreed with the special committee's findings, stating his belief in Pomeroy's guilt and calling attempts to explain the payment as something other than a bribe as "so improbable, especially in view of the circumstances attending the senatorial election, that reliance cannot be placed upon them." However, Thurman chose not to pursue the matter further, as March 3 coincided with Senator Pomeroy's last day in office. This whole matter was alluded to in detail in the satire by Mark Twain and Charles Dudley Warner, in which the prominent character Senator Dillworth is based on Pomeroy.
