The main Werribee Station building reflects two dramatic periods in its history. Details of its original form and construction are still evident in its form, materials and some architectural details. The impact of a fire in 1927 resulted in a reshaping of the building, with the walls reduced in height and a hipped roof replacing the previously gabled 'Cottage Orne' character. Other features - such as the integrated signal box - demonstrate developments in railway procedures and safe working systems.

During the 1980s and 1990s, the building suffered a sever decline in maintenance. Railway activities, such as ticket sales, have been moved out into portable structures. There is apparently some concern about the stability of the building's footings (although it is understood no detailed investigations have been undertaken). The stone work is also in need of specialist investigation to ensure it survives into the future.

The opening of the Geelong-Melbourne railway in 1857 provided a boost to the infant settlement of Wyndham Village (now Werribee township). The railway line ran through the village and a station was opened there.

The improvement in the district transport system provided a cheaper and more efficient way for local farmers to get their wiool and farm produce to market and encouraged the development of the small township. In 1851 the population of Wyndham Village was only 65 persons. They were scattered over a wide area and in 1854 there were "not more than ten or twelve houses in the village, one half of which consisted of the hotel and the adjacent tenements, the other half being located up and down the river at distances from the hotel varying from two to four miles. Growth was slow up to 1857, the population then numbering only seventy two persons". BY 1861, after the opening of the railway,the population had risen to 130 persons residing in 26 houses.

The opening of the Melbourne-Geelong railway was, in fact, a great event in the history of the whole colony. When the train reached Geelong on the first day, a grand banquet was held at which "eight tons of food (were) set out on three-quarters of a mile of tables".

Early maps of the Township of Wyndham show the Geelong to Melbourne Railway running through the town. It divides the Mambourin section of the township north of the line from the Deutgam section to the south.

Recent research into Werribee Railway Station by Andrew Ward, an architect who has specialised in the assessment of railway buildings, confirms that the design of this station is notable as a surviving example of the work of Edward Snell, the engineer/architect for the Geelong and Melbourne Railway Company. Snell also designed the Geelong terminal complex,which was only partly built and is believed to have been demolished over a century ago. As engineer, Snell was responsible for the design of the bridges and earthworks on the new railway, but these were reconstructed after the takeover of the company's assets by the colonial government in 1860.

 According to Ward, until recently it was thought that all the early Geelong and Melbourne Railway Company buildings and structures had been demolished. The survival of the Werribee Station, therefore, says Ward "may constitute the only known work of Edward Snell and it is certainly the only surviving remnant of Victoria's first company built railway line, preceding the oldest Government station building remaining at Williamstown by two years. Together with St Kilda Station of 1857, it is the oldest railway building in the state".

The St Kilda Railway Station, seriously damaged by fire is far from intact today. The Werribee Railway Station was also affected by fire. After it was burnt out in 1927, it was renovated in the style of the period with a cantilever verandah replacing the earlier standard VR late Victorian cast iron posted verandah. A photograph from The Sun News Pictorial of 17 May 1927 shows the damage caused by this fire.

Ward describes the architectural style of the original Werribee building as in form and detail in a "Cottage Orne" style popular for the homes of the gentry. This may have been linked with the Chirnsides who "would have been sensitive to this aspect". After the fire "the steeply pitched gable roof was replaced with a lower hipped roof but the masonry walls generally survive and are unique on Victoria's rail network for their use of sandstone quoining and window surrounds in conjunction with bluestone work of a quality generally inferior to later Government railway buildings".

Ward says that the "proportions of the windows and chamfered reveals" relate to the "Cottage Orne" style and "was only repeated in the VR network at Little River". However, Little River was designed and built by the Government after the 1860 takeover. He concludes that this choice of style may relate to the influence of the "squattocracy" of the district.

Thomas Chirnside reputedly offered land free of charge for the railway line providing the station was built at "The Werribee". After its opening, Chirnside often ran special  trains to bring his friends and supporters to coursing meetings, hunts, and other big occassions at Werribee Park. When he died, his coffin was taken by horse-drawn hearse to the Werribee Station. It was then carried by special train to Geelong for burial in the Eastern Cemetery. Mourners, staff and station hands travelled on the same train.

Werribee Railway Station became a focal point for the development of a central business area in the vicinity this century. Station and Watton Streets became desirable locations for hotels, banks and a variety of business premises. Nearness to the station and good rail transport was a popular selling point for township allotments. Today the station buildings are only partially occupied. However, they have been judged as of considerable architectural and historical significance and have been nominated to the Victorian Heritage Register. They have been classified 'A' by the National Trust.