The area presently known as Moulton Junction has had a convoluted history. Up until the mid-1940s, there were no bridges here, and no railroad junction actually existed here in any form until 1983. The only railroad track located here originally was the Wabash Railroad's line from Moberly, Missouri, which travelled north through present day Moulton Junction on its way to Des Moines, Iowa. North of this point, the Wabash passed over the Chicago, Rock Island, and Pacific Railroad's Golden State Route mainline that cut through Appanoose County on a generally east-west direction as it made its way through southeast Iowa and into Missouri. The Wabash crossed over the lower Rock Island tracks via a small bridge just west of the little town of Udell.
Southeast Iowa's topography consists of many high and low rolling hills that are divided by numerous ditches and creeks that lead into the various river systems. The original Rock Island mainline had many grades and curves as it wound its way in and out of the various high and low areas while traversing through this part of the state. In the early to mid-1940s, the railroad undertook a large reconstruction project under the direction of new CEO John D. Farrington, with the aim of straightening and leveling the mainline through southeast Iowa. Instead of going around the hills and valleys, the railroad would now go through them. Seven new segments of track were laid between Ainsworth and Centerville that shortened the line by several miles and considerably reduced grades and curves. Massive amounts of earth were moved as deep cuts were dug through the hilly country and huge earthen fills elevated the railroad high over many valleys. One of the new, deep cuts ran underneath the Wabash line here, at present day Moulton Junction, thus a new deck plate girder bridge was built to span the relocated Rock Island main. Presumably, this bridge was built sometime in 1945. The nearby gravel road was also re-routed to better cross the new railroad, creating two bridges in the area.
For all the work and new bridges, there was still no junction. The Rock Island had absolutely no need to interchange between its mainline and the Wabash in this area, so no connector track would climb its way out of the deep cut to get up to the Wabash tracks above. For nearly 40 years this state of affairs remained, but the coming decades would see big changes to the railroad landscape. The Wabash would become permanently leased to the Norfolk and Western Railway in 1964; blue Wabash diesels were soon replaced by all-black, high hood N&W units. Meanwhile, the Rock Island entered a period of steep decline that would ultimately prove fatal; the railroad turned its last profit in 1965 and entered into it's third and last bankruptcy in 1975. The Golden State Route that so much effort was spent on in the 1940s was left to rot, becoming so decayed that it was embargoed around 1978. By the time the railroad permanently ceased operations in 1980, the once proud mainline through southeast Iowa was just a shadow its former self, with rust-stained rails sitting unevenly on rotted and broken ties, rapidly disappearing underneath a sea of vegetation.
The death of the Rock Island and Burlington Northern's decision to abandon its own branch line to Centerville led to the creation of the Appanoose County Community Railroad (APNC) in 1983, and to the creation of Moulton Junction. To preserve rail access for industry in Centerville to the outside world, APNC purchased a small chunk of the former BN rail line running southeast from the city to where it tied into the former Rock Island Golden State Route trackage, which still lay abandoned, waiting for a buyer. The old Rock main was followed easterly to the point where it got close to the former Wabash line. Norfolk and Western Railway had merged with the Southern Railway just the year prior in 1982, forming the new Norfolk Southern Railway. A short and steep section of new track clawed upwards out of the deep Rock Island cut and gained level with the land the NS track sat on. A very sharp curve to the south was necessary to lineup the end of the APNC with the NS line; since this meant the APNC tracks would cross back over the old Rock Island cut, the railroad builders elected to fill in the area rather than install a curved bridge. Where the two railroads merged just south of the Norfolk Southern bridge, a small interchange yard was built. This allowed APNC locomotives to drop off their cars and run around them to get back to Centerville. Thus actual the creation of Moulton Junction came about in 1983.
Aside from the short section of track the APNC purchased in 1983 and a tiny section left in place at Fairfield, all the rest of the former Rock Island from Allerton to Ainsworth was removed in 1983. The Norfolk Southern overpass at Moulton Junction now just spanned an empty cut that soon became a swamp. The nearby road bridge proved unnecessary, and like many others that spanned the former Rock Island, it was soon torn out and filled in. Norfolk Southern rebuilt its line from Moberly to Des Moines in the 1980s, laying down new rail. Traffic experienced an upturn as new management in Des Moines acquired more business. However, in an effort to cut costs, NS abandoned the section from Moberly to Albia, Iowa, in 1994; the railroad elected for haulage rights with Burlington Northern to move freight to Albia, where it could then proceed up the joint NS/BN tracks to Des Moines.
Faced yet again with the threat of losing access to the national rail network, APNC quickly stepped in to buy the section of track from Moulton Junction north to Albia. Here the railroad finally found a permanent interchange with Burlington Northern, now BNSF Railway, via its east-west mainline. A short section of track was also saved south of Moulton Junction to Moulton, Iowa, apparently to serve a local elevator. Since nearly all of APNC's modest traffic was now heading north at Moulton Junction, bound for Albia, the junction was modified to a wye. Rail service to Moulton lasted but a short time before this was abandoned. The southern leg of the wye was removed, as were the tracks across the railroad bridge. Oddly, the section of interchange track south of the railroad bridge at Moulton Junction remains, even though it is completely cut off from the remaining APNC tracks. Rails from Moulton all the way up to this tiny section of track are also gone. Why the bridge and the abandoned tracks remain is a mystery. It is also unknown when this abandonment occurred, as there is no reference to it in the Iowa DOT Railroad Abandonment Log.
Although the bridge would sit semi-abandoned and out of service for approximately twenty years, this would not be the end of the story for this structure. In 2015, rails were relaid across the bridge and linked back up to the old interchange yard. The yard itself was cleared of all the small trees and undergrowth that had taken over in the two decades since it was last used. The area is now slated to become a tank car storage yard and trans-load facility, where product can be offloaded onto semi-tractor trailers for regional delivery. This means that the old Wabash bridge will now see active service once again, albeit in a limited fashion.
In 2016, Progress Rail leased the Appanoose County Community Railroad, creating the new Iowa Southern Railway.