Following the end of martial law and the destruction of the Ku Klux Klan, Upham for the most part returned to civilian life. However, his buildings and land holdings in Woodruff County were all ravaged to the point that he simply gave them up rather than stay there with all the hatred and ill will that was directed towards him. Instead, he and his wife moved to Little Rock where he took up a new life.

In Little Rock, Upham and his wife adopted a little girl. Upham himself invested in real estate and stayed in the state militia. In October, 1870, Upham was appointed brigadier general in the state militia and placed in command of the Seventh Military District in Central Arkansas. In 1872, there was a flare-up of violence in Pope County as a Klan-like terrorist group literally declared war on everyone who did not fully agree with white supremacy. Governor Ozra Hadley apponted Upham as major general in command of the entire Arkansas militia. Pope County was placed under both martial law and was occupied by militia units from several other counties. During a series of engagements in Pope County, the terrorists were defeated and Pope County was restored to civility.

Upham also distinguished himself in politics. Upon arriving in Little Rock, he became a clerk in the Pulaski County Chancery Court. Not content with merely becoming a clerk, Upham ran for both the Little Rock City Council and the Little Rock School Board and won both elections. In both of these positions, Upham became the leader of those legislative bodies so much so that he was often accused of being the "dictator" of Little Rock. As prominent as Upham's roles in both Little Rock and Woodruff County were, the highest ranking position that he would ever hold was yet to come.

In 1876, the position of United States Marshal for the Western District of Arkansas became open. This district included not only Western Arkansas, but also the Indian Territory that is now known as the state of Oklahoma. Despite the fact that Upham had never lived in that district, President Ulysses S. Grant appointed Upham to that positon. Upham's appointment received mixed reviews. The Independent Arkansian newspaper called him "as grand a rascal as ever went unhung." On the other hand, the Fort Smith newspaper Wheeler's Western Independent called Upham an "efficient officer" whose "business in his department will meet promptness and dispatch." Upham promptly went about his business cleaning up corruption in the district court's jurisdiction. Upham also forced the prisoners to clean up the town of Fort Smith. In 1879, there was a dispute between Republican President Rutherford B. Hayes and the Democratic House of Representatives led by Speaker Samuel Randall of Pennsylvania that led to the stoppage of the funds necessary to keep the Federal district court functioning. Upham contributed the funds from his own pocket to keep the district court in session. This was significant since all of the oher district courts shut down due to the lack of funds.

Despite Upham's public service, President Hayes declined to reappoint him. Shortly thereafter, Upham's health began to decline and he decided to take one last visit to Massachusetts. There, in the town of Dudley where he had been born fifty years earlier, Upham passed away from tuberculosis. He was buried at Oaklawn Cemetery in Little Rock and both his wife and stepdaughter are buried next to him.

When Upham was the U.S. Marshal, Judge Isaac C. Parker was the "hanging judge" who presided over the Federal District Court.