Pacific Junction was established by the railroad in 1871 to serve as the western terminus of the Burlington and Missouri River Railroad, the eastern terminus of the Nebraska Burlington & Missouri River RR, and a station on the Kansas City, Council Bluffs, & Saint Joseph Railroad. All three were consolidated as part of the Chicago, Burlington and Quincy Railroad, today's BNSF. After several rough and tumble years of growth Pacific Junction was incorporated in 1882. The scene of violence during the Burlington Railroad Strike of 1888, PJ's population peaked during the early 20th century with just over 700 people. Railroad traffic through town remains almost constant although the town's connections to the railroad have declined significantly since 1971. Historic structures include the 1914 Pacific Junction Public School which graduated its last high school class in 1961 and closed for good in 1986.
Pacific Junction was impacted by the 2019 Midwestern U.S. floods. Buyout funding has been allocated for local residents