The original Fairfax Station was constructed in the mid-1850s by Irish immigrants. Many of these people had recently arrived during the late 1840’s – early 1850’s and were immediately employed by the Orange and Alexandria Railroad Company, which had been chartered by the Virginia General Assembly in 1848 to construct a rail line from Alexandria to Orange County, Virginia. Enterprising businessmen sought a cheaper and more efficient transportation alternative to the turnpikes and stagecoach lines to move farm products to the coastal markets and for export. The line reached present day Manassas (then called Tudor Hall and subsequently Manassas Junction) by October 1851 and was officially completed to Gordonsville in Orange County by March 1854. It was so successful that the rail line was further extended to Lynchburg, Virginia by 1860.

Many of the Irish immigrants who had worked on this rail line ultimately settled in the surrounding area of Fairfax Station helping to create the small community that became the station's namesake. St. Mary’s Church, approximately ¼ mile, away was constructed by 1858 and was the parish for many of these new settlers. Fairfax Station was the railroad station for the town of Fairfax, then known as Fairfax Court House. The rail station purposely was located 2 ½ miles from the town. Many of the local residents did not want these smelly, smoky, noisy, fire breathing contraptions close to the town, and the railroad company was very willing to construct the rail line away from the town where land was cheaper.

Until the Civil War this was a sleepy little rail line taking supplies, freight, and passengers between Northern Virginia and the central portion of downstate Virginia. A normal transportation day on the rail line before the war would include no more than a few trains. During the Civil War this rail line and the station were of great strategic importance. As a main line to Central Virginia, the Orange and Alexandria line was the most direct and easiest way to get troops from Alexandria to Richmond (The O&A intersects the Virginia Central in Gordonsville). With the same track gauge, it would be easy to get to Richmond. Both armies knew this and either planned their attacks or defensive postures accordingly. Consequently, during the first 3 ½ years of the war many battles were fought over and along this rail line. Central to the station's historical significance are the concurrent Civil War battles of Second Manassas and Chantilly.

Serving first as a supply base for Union forces during the summer of 1862, Fairfax Station became a center for emergency treatment and evacuation of the wounded to hospitals in Alexandria and Washington after these two major battles. Clara Barton attended many of 3,000+ wounded Union soldiers who lay on the hill between the historic St. Mary's Church and the depot. As the Union Army vacated the area in and around Fairfax Station, the depot, remaining rail cars and supplies were ordered destroyed by Col. Herman Haupt, United States Military Railroad, Colonel and Chief of Transportation. Union troops later rebuilt the station.
In the years of peace that followed, Fairfax Station started to slowly prosper. The second railroad station created by the Union Army in late 1862 was torn down and a new modern station replaced it in 1879. Ultimately, this station became the primary railroad station serving the growing county seat, the Town of Fairfax. By 1891, yet another new train station was needed and it was the first station located north of the tracks. Finally, in the early 1900’s, the rail line was double tracked, requiring construction of the fifth and final train station. It served the increasingly prosperous town of Fairfax long after WWII.

Many rail company mergers and reorganizations occurred from the late 1860’s until June 1894, when this line adjacent to Fairfax Station became part of the mighty Southern Railway. Southern operated this rail station very successfully until late in the 1950’s when automobile travel and trucking companies started taking more and more passenger and freight business away from the rail line. By 1973, Southern Railway no longer operated this rail station profitably and closed the station, which was the last operating railroad station in Fairfax County.

In 1975 a group of concerned citizens began efforts to save the old depot. With Southern Railway's donation of the building and financial and volunteer assistance from local groups, the Friends of Fairfax Station, Inc. reconstructed the station on donated land just up the hill from the original site. It now serves both as a museum of Civil War, railroad, and local history and as a bustling community center.
The museum houses Civil War, Red Cross, and historic railroading memorabilia as well as a variety of artifacts found in and around the old station. In more recent years, many donors have added to the historic items in the museum.

In 1975 a group of concerned citizens headed by Lena Wyckoff and the Clifton Community Woman’s Club began efforts to save the old depot.

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