Born in Bennington, Vermont, Naper traveled with his parents during his youth to Ashtabula, Ohio, where he helped his father, who was a ship builder. The Naper ships plied the Great Lakes with Fort Dearborn on Lake Michigan being one of the ports they regularly visited. On an early trip, Naper acquired lots near the fort, as did many of the first settlers to reach the Chicago River port.
On a later trip, in 1831, on the Telegraph, a ship Captain Joseph Naper built, he was joined by his brother, John Naper. Both families and five other families settled in the area, first known as Naper's Settlement, which later became a part of DuPage County. Joseph platted the town of Naperville, surveying the property and was elected to the Illinois House of Representatives for the first time in 1836. Here he laid the groundwork and supervised passage of the bill which broke DuPage County away from Cook County in 1839. Also serving on the committee was Abraham Lincoln, then a newly elected legislator from the Springfield area.
Joseph Naper returned to the Illinois General Assembly in 1852. His actions again provided a means for establishing new communities in the State of Illinois.
He served as a captain in the Black Hawk War of 1832 and was one of the many DuPage County men who served in the Mexican War of 1846. Naper became the first village president of Naperville in 1857.
He was one of the stockholders in the "Old Plank Road", which improved transportation between Aurora, Illinois and Chicago. Another major stockholder was Colonel Julius M. Warren of nearby Warrenville. As with many of the early pioneers, Naper engaged in a number of businesses and trades as he helped in the development of the new county.
Joseph Naper's sister, Amy Naper, was married to John Murray, who was one of the original founders of Naperville, Illinois.