When the War began in the spring of 1861 and Arkansas seceded from the Union, Newton entered the Confederate Army as a captain and in May, 1862 was appointed as a major, serving as the Adjutant General on the staff of Major General Thomas C. Hindman, commanding the Department of the Trans-Mississippi and the District of Arkansas. In this post he assisted Hindman in the raising and training of troops for defending the state, as the departure of General Earl Van Dorn and his Army of the West had completely emptied Arkansas of troops and military supplies.

In April 1863, Newton raised and was appointed as a colonel to command the 5th Arkansas Cavalry Regiment, which he led as part of General Walker's Arkansas Cavalry Division during the battle of Helena and in the Little Rock Campaign in the summer of 1863. In August, 1863, Newton's regiment conducted screening operations in front of the Confederate defenses along Bayou Meto, and guarded Shallow (or Shoal) Ford on that bayou. Pushed away from Bayou Meto by the federal cavalry after the Union repluse at Reed's Bridge, Newton continued to harass the federals as they searched for an alternate approach to Little Rock.

After the war, Colonel Newton returned to Little Rock and reopened his law practice, forming a partnership with former Major George A. Gallagher with his offices at 118 West Markham Street.

In 1874, Elisha Baxter, now a Republican, was elected governor in a hotly contested election. Baxter then appointed R.C. Newton as a major general in the Arkansas State Militia. Baxter proved a disappointment to the Radical Republicans and carpetbaggers who had helped him get elected, as he soon displayed that he was no man's puppet and attempted to serve the needs of the common people. Joseph Brooks, an opponent of Baxter in the general election, seized the State Capitol and ousted Baxter from office by force of arms. Baxter still held many of the reins of state government, and began to rally his supporters to suppress the attempted coup. General Newton became commander of the militia troops supporting Baxter in what became known as the "Brooks-Baxter War", and led them in a number of skirmishes and battles in which nearly 100 militiamen on both sides were killed.

Governor Baxter was able to regain the Capitol and the Governor's Office after several weeks, and in gratitude for his service, appointed General Newton as the State Treasurer following the overthrow of the carpetbag government in Arkansas. General Newton died at Little Rock on June 5, 1887 at the age of 48. He is buried at Calvary Cemetery in Little Rock.