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In 1849, the newly formed Sydney Railway Company applied to the government for four blocks of land between Hay and Cleveland streets to construct a Sydney Railway terminal. Although the Surveyor General favoured Grose Farm (now the grounds of the University of Sydney), which was further from the city and less costly to develop, the company was finally granted land in the Government Paddocks between Devonshire and Cleveland Streets for the construction of the first Sydney railway terminus which was located there from 1855. The first station included timber and corrugated-iron station buildings, an engine shed, carriage shed and goods sheds. A branch line to the Darling Harbour wharves and goods yard ran from the western side of the rail yard. The overbridge that carried Parramatta Road across this line remains as the oldest piece of railway infrastructure in the NSW system.

The position of the station was at the southern end of the town, at the point where journeys into the interior of the colony began. With the addition of the new railway station, this part of the town grew in importance as an entry point to the city. Shops began to be built around the station and in the adjacent streets. By the turn of the twentieth century, major department stores were positioned in George and Pitt Streets to take advantage of the growing number of commuters coming through the area. This was particularly the case after 1879 when the first steam tramline to the station was installed, linking it with the Hunter Street in the city.

As the importance of the railways increased, the station and the Sydney Yard attached to it were also extended. A new sandstone engine house was constructed in 1866 on the eastern side.

In 1869, the Mortuary Station was constructed in the western yard, to connect to the new general cemetery at Rookwood. The station, designed by Colonial Architect James Barnett, provided a siding with an elaborate gothic station building, which included a chapel and waiting rooms, for the transport of coffins and mourners to the cemetery where a sister receiving station had also been constructed. Mortuary Station at Sydney is the only surviving example of such a station in situ in the NSW system and is a rare survivor of the first phase of the Sydney Yard. Mortuary Station is written about in more detail on a separate listing .

In 1876 the original Central Railway Station building was replaced by a new brick station building (the second station). John Whitton, the Engineer-in-Chief, designed a neo-classical station building to be constructed of brick with decorative detail using polychromatic and relief work.

Almost immediately the demand for platform space during peak times resulted in additional branch lines and platforms being constructed adjacent to the original passenger station.

Between 1876 and 1902, Whitton's second station group and the yard were undergoing constant upgrades and expansions, with the addition of carriage sheds, goods sheds, workshops, new sidings and other railway infrastructure. At its peak there were 13 passenger platforms in the 1876 station as well as the Mortuary Station on the western edge of the yard. By 1890 Whitton's station building had become engulfed within a sea of sheds and platform canopies.

In 1888, the then Railway Commissioner, Edward MG Eddy began work on the quadruplification of the Western Line to Homebush and the duplication of other suburban lines. As part of this project he proposed a new Sydney terminal station closer to the city. The first proposal was for a station in King Street in the city. This would have resulted in large-scale demolitions and resumptions, including much of Hyde Park. Eddy submitted an alternative proposal in 1891 for a site north of the existing station on the land occupied by the former Devonshire Street cemetery (closed to burials since the 1860s), the Benevolent Asylum (c1818) and a police barracks. This site was chosen for a new grand station complex to be built, not least as it was already in government hands and largely devoid of major structures.

Work began on the third Sydney station, Central Railway Station, in 1901, with the removal of the cemetery being the first priority. The bulk of the construction work occurred between 1902 and 1906, including the exhumations, excavations, demolition of buildings on the site and construction of the station. The construction work began in mid 1902, with the foundation stone being laid on 30 April 1902 by the Secretary for Public Works, the Hon EW O'Sullivan. By mid 1903 it was reported that the general earthworks were completed and work on the various subways was underway, with a second foundation stone at the base of the clock tower being unveiled in September 1903.

The station was officially opened on 4 August 1906 despite the main building not being completely finished. Construction had only been completed as far as the first floor, but included all the underground subways for the transfer of luggage and mail as well as pedestrian subways (Devonshire Street tunnel). The new station had moved one block north from the previous incarnations, closer to the city. If Belmore Park is included, all the land now occupied by the railway at Central and Redfern coincides with the Sydney Railway Company's original selection of four blocks between Hay and Cleveland Streets.

The main terminal building was built using Pyrmont sandstone to a design of the Government Architect WL Vernon. A feature of the design was the deliberate separation of passenger, vehicle, train and tram services, all of which entered the station from different levels and directions, eliminating the danger of accidents which had been a feature of the previous station arrangements. The new design created a multi-level transport interchange, able to handle major traffic and pedestrian flows effectively and safely. The trams entered the station via two underbridges at the western and eastern ends of Eddy Avenue. The eastern-end underbridge was a steel bridge with decorative ironwork balustrades and a riveted steel plate girder. It remains as a rare piece of Sydney's original tramway infrastructure and since 1997 has been in use for the Sydney light rail system.

Another feature was the prominent positioning of the station at the southern end of the city. The relatively low rise of the city at the time of the station's completion meant it was a major landmark, visible from much of the city. The inclusion of the existing Belmore Park in the wider railway complex design, the planting of gardens on the western side facing George Street and the main vehicle entrance, and the location of Prince Alfred Park to the south of the new station placed the complex in a garden setting, further enhancing its status as a city landmark.

From the time of opening, work continued on both the station building and the Sydney Yard associated with it. In August 1906 Platforms 9 and 10 were opened, while overhead signal boxes were opened as lines and platforms were completed. At first, four signal boxes were required, using a mechanical system of signals. These were reduced to two boxes from 1910 when electro-pneumatic technology was introduced. By the early 1920s, a complicated series of lines, cross-overs, junctions and points was in place directing trains in and out of the station and yard complex.

In 1921 the clock tower was completed with the clock beginning to operate from March of that year. The clock tower was the last of the major built elements in the first phase of the station to be completed. The top of the dome sits 64.3 metres above the concourse or 85.6 metres above mean sea level. Even more so than the station itself, the clock tower became a major city landmark, with the clock being utilised by workers in the surrounding factory districts as their daily time piece, earning it the nickname 'the worker's watch'.

In 1915, before work on the main station was completed, the first extension began. Following recommendations for a city railway system and underground network from a royal commission into Sydney's planning in 1909, approval was given via the City and Suburban Electric Railways Act, 1915, to begin construction on a suburban electrification and underground railway. Although excavations got under way in late 1916, they ceased in 1918 as funds were diverted away from the project into the war effort. Work resumed in earnest in February 1922. A new entrance at Elizabeth Street was constructed to serve the electric platforms. The entrance was built using sandstone to match the main station, with four ionic columns as features. New baggage subways and electric lifts were also installed and linked to the existing tunnel network.

Eight new platforms were built to the east of the original 1906 station platforms at a higher level to take the new electric trains between 1922 and 1926. These platforms were named 'Central' to distinguish them from the 'Sydney' or steam-train platforms.

As well as new entries, subways and platforms, a complicated series of flyovers was built to carry the new electric lines. The flyovers were built using steel beams on brick piers with large concrete foundations. As part of their construction, an old carriage shed and several storage sheds were demolished, while an old sewer was also diverted. The flyovers allowed for trains on the Up line (heading towards Sydney) to go up and over trains on the Down line (heading away from Sydney) without interfering with each other or requiring point cross overs. When completed, this was the largest collection of flyovers in the world.

Adjacent to the northern end of the flyovers, on the eastern side, a new substation was built in 1925-26. Known as the Prince Alfred substation, it was constructed as part of the electrification of the suburban lines. The substation was one of fifteen built for the electrification between 1926 and 1932, and one of three 'Bradfield' designs, the other two being at Meeks Road (Marrickville) and Hurstville, both of which remain in use.

The first electric train ran from Central Station on 1 March 1926. In December the new line to the first section of the Sydney underground also opened, with trains to Museum and St James. The underground system required the construction of new underbridges from Central north across Eddy Avenue, Hay and Campbell Street. This bridge was built using an innovative combination of 5-span continuous reinforced concrete beams with variable depths that creates the impression of arch construction. This was a pioneering and complicated use of reinforced concrete in railway bridge design.

A change in train locomotion technology began to appear at Central from the 1940s, when four diesel-electric shunting engines were leased from the US Army, originally intended for work at the munitions factories but utilised instead by the NSW Railways in the Sydney Yard. Two were eventually acquired outright in 1948, with the other two transferred to Commonwealth ownership. In 1951, the first diesel electric locomotive on main line service was introduced in NSW. Initially only on goods trains, from 1955 dieselisation of passenger trains began to replace steam. The last steam train on a regular service left Central in October 1969. The end of steam saw the removal of much of the associated infrastructure such as water columns, water tanks, coal hoppers and storage.