At the outbreak of the war, Bramlette put his promising political career on hold and enlisted in the Union Army, raising and commanding the 3rd Kentucky Infantry.

Within a year, however, federal policies such as recruiting Kentucky African-Americans for the Union Army and suspending the writ of habeas corpus for Kentucky citizens caused Bramlette to abandon his support of the Lincoln administration and declare that he would "bloodily baptize the state into the Confederacy".

[6] He returned to Louisville to accept President Abraham Lincoln's offer to become United States District Attorney for Kentucky.

[4] In December 1863, Bramlette addressed the General Assembly, declaring that the state had fulfilled its quota of soldiers for the Union army.

[10] Although Bramlette assumed the governorship as a staunch supporter of the Union cause, within a year he issued a proclamation that he would "bloodily baptize the state into the Confederacy".

[10] With the goal of enlistment of Kentucky blacks into the Union Army, Lincoln authorized a special census in 1863 which showed 1,650 freemen and 40,000 enslaved males of military age.

[11] By April, enslaved men, despite the stipulation of owner consent and motivated by the prospect for their emancipation, fled to enlist.

[12] The situation worsened when on July 5, 1864, President Lincoln suspended the writ of habeas corpus for citizens of the Commonwealth.

[13] Burbridge continually menaced Kentucky's citizens, interfering with the presidential election of 1864, and banishing Lieutenant Governor Richard T. Jacob from the state.

[14] The General Assembly petitioned new president Andrew Johnson to call an end to martial law in the state.

President Johnson received the message, ending martial law and restoring habeas corpus in Kentucky.

[14] When the General Assembly convened in December 1865, Bramlette sought to restore harmony in the state by issuing pardons to most ex-Confederates.

[14] He and the majority of the General Assembly opposed passage of the Fourteenth and Fifteenth amendments, and Bramlette protested the establishment of the Freedmen's Bureau in the Commonwealth.

[13] Bramlette was very proud of those of his accomplishments not related to the Civil War, including the reduction of the state's debt and the establishment of the Agricultural and Mechanical College (later, the University of Kentucky).