Phelps returned to the United States Senate on January 17, 1853, having been appointed to fill the unexpired term of Senator William Upham, who had died. He served until March 16, 1854 when the Senate resolved that he was not entitled to the seat on the grounds that he had been legally appointed by the Governor of Vermont when the Vermont General Assembly was not in session, but once the legislature was in session, it was incumbent on legislators to choose a successor.