Pope was born in Louisville, Kentucky to an prominent family in regional politics. In 1806, he graduated from Transylvania University in Lexington, Kentucky. He then studied law, was admitted to the bar, and settled in Ste. Genevieve, Missouri, in 1804, where he commenced the practice of law in the Louisiana Territory, which had recently become part of the United States as part of the Louisiana Purchase.

When Illinois Territory was organized in 1809, the influence of Pope's family, especially that of his brother, John, U.S. Senator from Kentucky, helped Pope to become appointed as Secretary of the Territory by President James Madison on 23 February 1809. The Pope family influence also resulted in Pope's cousin, Ninian Edwards, being appointed as Territorial Governor. Pope moved first to Vandalia and then to Springfield. He was reappointed in 1813 and served until 1816, when he resigned after being elected September 5, 1816 as Territorial Delegate to the United States Congress. He served as Delegate in the Fouteenth and Fifteenth United States Congresses.

Illinois was admitted as a state while Pope was in Congress, and he was instrumental in adjusting the northern boundary of the state from the southern extremity of Lake Michigan to 42° 30', thus adding the territory now included in the thirteen northern counties.

Upon leaving Congress, he was appointed register of the land office at Edwardsville, Illinois, on November 30, 1818, and served until March 3, 1819, when he was appointed United States judge for the District of Illinois. He served in that capacity until his death. He was an unsuccessful candidate for election to the United States Senate in 1824.

Pope died in St. Louis, Missouri and is interred in the Colonel O’Fallon Burying Ground, on the Bellefontaine Road. His son, was General John Pope and he had a nephew, Daniel Pope Cook, who was also prominent in Illinois politics.

Pope County, Illinois and the Nathaniel Pope Elementary School in North Lawndale, Chicago are named for Pope.