What is now the lower level of Route 139 was originally designated as the northernmost part of Route 1 Extension, which was authorized by the New Jersey Legislature in 1922, a route that was to extend the existing Route 1 from Elizabeth to the Holland Tunnel in Jersey City. When the U.S. Highway System was established in 1926, this road was also designated as part of U.S. Route 1. In the 1927 New Jersey state highway renumbering, this highway became part of Route 25, a route that was to run from the Ben Franklin Bridge in Camden to the Holland Tunnel.
thumb|left|View east along the lower level of Route 139 just after passing under CR 501 (JFK Boulevard) in Jersey City
In the 1953 state highway renumbering, Route 25 designation was changed to U.S. Route 1/9 Business from the Pulaski Skyway over Tonnele Circle to the Holland Tunnel. By the 1990s, U.S. Route 1/9 Business was renumbered to NJ Route 139. Along with the Pulaski Skyway, most of the Route 139 lower level became a contributing property to the Route 1 Extension historic district listed with the state and federal registers of historic places in 2005. Route 139 and I-78 were designated as concurrent where the roads joined at the Holland Tunnel approach near Jersey Avenue all the way to the New York state line in the Holland Tunnel. The four-lane, westbound, , 14th Street Viaduct, which was connected to the 12th Street Viaduct, was opened on February 13, 1951. The Port of New York Authority, which superseded the two state tunnel commissions and took over authority for the Holland Tunnel in 1930, built the 14th Street Viaduct in order to avoid the turns to and from Jersey Avenue, but turned over authority over the viaduct to the New Jersey State Highway Commission. <!--NY Times shows NO SPACE for NY TimesSpecial. could not find online article at NY Times Archive. had to go thru bccls.org, which requires library card number log in!?--> The western end of 12th Street Viaduct was transitioned from two-way traffic to one-way, four-lane, eastbound traffic just east of the connection with the westbound 14th Street Viaduct. The upper level of Route 139 (Hoboken Avenue Viaduct), which provided a multi-lane thoroughfare from Palisades Avenue to John F. Kennedy Boulevard, was also opened. This proposed highway was strongly supported by Jersey City Mayor Bret Schundler, who felt that the road could bring further development, as well as provide traffic relief to the four-lane Route 139. In 1998, this project was allocated $26 million in the federal Transportation Equity Act for the 21st Century. Both Jersey City mayor candidates in 2001 supported a transit line instead of a highway along the Bergen Arches. Plans for a highway along the Bergen Arches were dropped in 2002 as leaders of Jersey City, including Mayor Glenn Dale Cunningham, favored mass transit.
In a controversial move in 2011, Governor Chris Christie directed the Port Authority of New York and New Jersey to divert money originally earmarked for the Access to the Region's Core rail project to highway projects. The agency agreed to pay $1.8 billion to partially fund rehabilitation to the Pulaski Skyway and Route 139, and other projects that it considers part of the larger distribution network in the Port of New York and New Jersey.
The Route 139 project rehabilitated the eastbound side of Hoboken Avenue Viaduct and resurfaced the westbound roadway. There were operational improvements at several intersections on the upper roadway, replacing all overpasses. It also replaced the deck and rehabilitated the superstructure of the Conrail Viaduct. The total project cost was estimated at $180–200 million and was expected to be completed by 2016, then later pushed back to 2019. The Pulaski Skyway reopened in mid-2018, and the lower level of Route 139 was temporarily restored to four lanes in December 2018, but was partially closed again in early 2019. Improvements added to Route 139's lower level in 2019 included new lighting and new pavement markings.
The section of 12th Street east of Marin Boulevard, which carries the eastbound I-78 and Route 139 toward the Holland Tunnel in Jersey City, was narrowed from six to four lanes after open road tolling was implemented at the Holland Tunnel. Subsequently, in 2025, the United States Department of Transportation awarded a $25 million grant to the Port Authority of New York and New Jersey to narrow the stretch of 12th Street between Jersey Avenue and Marin Boulevard.