He remained loyal to the national government during the American Civil War and won reelection to a third and final term in the House in 1862, having been redistricted to the 3rd congressional district in the interim.
[2] A Unionist, Noell proposed a plan for compensated emancipation in December 1862, wherein the United States government would pay loyal slaveholders a combined sum of $10 million over a period of 30 years; as a further condition, he proposed that freed people be colonized outside the United States.
[3] Noell was one of two slave state members to serve on a select committee of the House that produced the Confiscation Act of 1862.
[4] In an address to the House on December 17, 1862, he impugned his former colleagues in the Democratic Party for their reluctance to support the aggressive prosecution of the war.
He denounced proposals for a negotiated peace and ridiculed the belief that slavery and the Union could both be preserved, stating, "when slavery comes in as an element of rebel strength, and the question is presented between its perpetuation and the preservation of the Union, then let the former die.