Paynter served in the Senate from March 4, 1907, to March 3, 1913. He was not a candidate for reelection in 1912. In the Senate he served as chairman of the U.S. Senate Committee to Examine Branches of the Civil Service. After his career in politics, he moved to Frankfort, Kentucky in 1913 to continue the practice of law and follow agricultural pursuits. He died in Frankfort and was interred in the State Cemetery.