In 1850 a company was formed to construct a steam railway from Geelong to Melbourne to be completed within three years. The company collapsed due to lack of financial support within two months. Shortly after, Mt Alexander and Murray River Railway Company announced its intention to build the line to those places.

Thomas Chirnside, when he learned of the plan, offered land free of charge as long as a station was built at Werribee. It would be, among other things, a cheaper form of transport to take wool to the markets.

In 1853, the Governor travelled down to Geelong by steamer to cut the first turf of the Railway and lay the foundation stone of the Geelong station. A sealed bottle containing an appropriate message, gold, silver and copper coins was placed under the stone.

Contracts were let for the construction of the railway, including a jetty at Geelong and bridges over the Little and Werribee (or Exe) Rivers. To ease the existing labour shortage because of the Gold Rush, the Government in June 1854 hired 100 prisoners to the company at five shillings each daily. The prisoners were housed in one of the penal hulks brought from Williamstown and moored in Corio Bay. Convicts who worked on the railway are said to have been locked up at night under the bluestone building of the Little River Railway Station. The station building was completed in 1864.

By October 8, 1856 the permanent rail line extended ten miles from Geelong to beyond Duck Ponds (Lara) and on 14th October a trial passenger trip was made. From 1st November a mixed train service operated twice daily between the two places and in 1857 it was carried on to Little River and then to Werribee.

On 25th June 1857 the railway line was opened as far as Greenwich (Newport). Passengers had to walk down the pier and get on a steamer to be conveyed to Melbourne. The station at Newport was originally called 'Geelong Junction' then 'Willliamstown Junction'.

In 1858 the terminus moved forward to Williamstown Pier. Then in the following year, after construction of a river bridge, the Government built railway between Melbourne and Williamstown was opened.

Passengers could now travel by privately owned railway from Geelong to Williamstown Pier, then by Government railway to Batman's Hill (Spencer Street). By April 1860, the Geelong and Melbourne Railway Company was in financial difficulty and was bought out by the Government.

At first no goods were carried by train because no sheds or loading spaces were provided at the terminus at Newport. The trains only ran in the daytime as most of the line was single track and unfenced and cattle could easily wander onto the track making travelling at night dangerous.

In 1876 there was an attempt to wreck the passenger train from Geelong which was actually carrying horses for the Flemington Races. A section of rail was laid across the railway line at Skeleton Creek which the train hit at top speed. The engine was damaged but the train was able to continue to Newport. It was suspected that someone wanted to stop the horses from competing in the races, and a reward was offered for the conviction of the persons responsible but no one was ever brought to justice.

On April 4, 1884, the Geelong Advertiser reported a frightful train crash between Werribee and Little River. Three people were killed and 20 were injured. An inquiry subsequently revealed that the collision between the passenger train from Geelong and the goods train from Melbourne, was caused by an incorrect telegram sent by the daughter of the Werribee stationmaster, Mr Biddle. Thomas Biddle had left his daughter in charge of the station whilst he attended choir practice. He was charged with manslaughter but not found guilty. As a result of the accident, the Government paid 23,000 in compensation.