1852 - 1890
The company was incorporated on November 10, 1852 as the Grand Trunk Railway Company of Canada to build a railway line between Montreal and Toronto, however the charter was soon extended east to Portland, Maine and west to Sarnia, Ontario. In 1853 the GTR purchased the St. Lawrence & Atlantic from Montreal to the Quebec-Vermont border, and the partner company Atlantic & St. Lawrence through to the harbour facilities at Portland. A line was also built to Lévis, via Richmond from Montreal in 1855, part of the much-talked about "Maritime connection" in British North America. In the same year it merged with the Toronto and Guelph Railroad Company, the latter's railway was already under construction. But the Grand Trunk Railway Company changed its original route and extended the line to Sarnia, a hub for Chicago-bound traffic. By July, 1856 the section from Sarnia to Toronto opened, and the section from Montreal to Toronto opened in October of that year. By 1859 a ferry service was established across the St. Clair River to Fort Gratiot (now Port Huron, Michigan). This service was later replaced by the St. Clair Tunnel, which was opened for railway traffic in September 1891.

By 1867, it had become the largest railroad system in the world by accumulating more than 2055 km of track that connected most of the east coast from Portland Maine and the three northern New England states with the Canadian Atlantic provinces with much of Lower and Upper Canada (Quebec and Ontario) west as far as Port Huron Michigan through Sarnia Ontario. By 1880, the Grand Trunk Railway system stretched all the way from the Atlantic Ocean in the east as far west as Chicago, Illinois, and still fell under the corporate structure of a single company.

Several impressive construction feats were associated with the GTR: the first successful bridging of the St. Lawrence River on August 25, 1860 with the opening of the first Victoria Bridge at Montreal (replaced by the present structure in 1898); the bridging of the Niagara River between Fort Erie, Ontario and Buffalo, New York; and the construction of a tunnel beneath the St. Clair River, connecting Sarnia, Ontario and Port Huron, Michigan. The latter work opened in August, 1890 and replaced a ferry at the same location - the GTR system's mainline having been extended west to Chicago by operating as the Grand Trunk Western Railroad (Port Huron-Chicago).

Common during 19th century railway construction in British colonies, GTR built to a broad gauge (Provincial Gauge) of 5 feet, 6 inches (1676 mm), however this was changed to the standard gauge of 4 ft 8.5 in (1435 mm) by 1873 to facilitate interchange with U.S. railroads.

The GTR system expanded throughout Southern Ontario, Western Quebec, and the state of Michigan over the years by purchasing and absorbing numerous smaller railway companies, as well as building new lines. GTR's largest purchase came on August 12, 1882 when it bought the 1371 kilometre Great Western Railway, running from Niagara Falls-Toronto, and connecting to London, Windsor, and communities in the Bruce Peninsula.

By 1880, the GTR stretched from the Atlantic port of Portland, Maine to Chicago, Illinois with its line west of the St. Clair River being operated as the GTWR. The company also sold a line along the St. Lawrence River between Riviere-du-Loup and Levis in 1879 to the federal government-owned Intercolonial Railway of Canada (IRC), and granted running rights in 1889 to the IRC on trackage between Levis and Montreal.
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1890 - 1923

As the dominant railway in British North America, GTR was reportedly asked by the federal government soon after Confederation to consider building a rail line to the Pacific coast at British Columbia (B.C.) but refused, forcing the government to enact legislation creating the Canadian Pacific Railway (CPR) to meet B.C.'s conditions for joining Confederation. By the early 1900s, GTR desired to operate in Western Canada, particularly given the virtual monopoly of service that CPR maintained and the lucrative increasing flows of immigrants west of Ontario. The federal government encouraged GTR to cooperate with a local railway company operating on the Prairies, the Canadian Northern Railway (CNoR), but an agreement was never reached.

CNoR decided to build its own transcontinental system at this time, forcing GTR in 1903 to enter into an agreement with Wilfrid Laurier's government to build a third railway system from the Atlantic to the Pacific. GTR would build (with federal assistance) and operate the Grand Trunk Pacific Railway (GTPR) from Winnipeg, Manitoba to Prince Rupert, British Columbia, while the government would build and own the National Transcontinental Railway (NTR) from Winnipeg to Moncton, New Brunswick via Quebec City, which the GTR would also operate.

The routing of these systems was extremely speculative as GTPR's main line was located farther north than the profitable CPR main line in the Prairies, and NTR was located even farther north of populous centres in Ontario and Quebec. Construction costs on the GTPR escalated, despite having the most favourable crossing of the Continental Divide in North America at Yellowhead Pass. GTR's cost-conscious president Charles Melville Hayes was one of the victims onboard RMS Titanic on April 15, 1912. His death is speculated to have contributed to poor management of GTR over the ensuing decade, and also contributed to the abandonment of the uncompleted Southern New England Railway to Providence, Rhode Island, begun in 1910.

Construction started on the GTPR/NTR in 1905 and the GTPR opened to traffic in 1914, followed by the NTR in 1915. It was a transcontinental system, with the only exception being the NTR's ill-fated Quebec Bridge which would not be completed for several more years.

The first indication the arrangement with the government was faltering came when GTR refused to operate the NTR, citing economic reasons. With the enormous cost of building the GTPR and the limited financial returns being realized, GTR defaulted on loan payments to the federal government in 1919. GTPR was nationalized on March 7 of that year, being operated under a federal government Board of Management until finally being placed under the control of the Crown corporation Canadian National Railways (CNR) on July 20, 1920.

GTR underwent serious financial difficulties as a result of the GTPR, and its shareholders, primarily in the United Kingdom, were determined to prevent the company from being nationalized as well. Eventually on July 12, 1920, GTR was placed under control of another federal government Board of Management while legal battles continued for several more years. Finally, on January 20, 1923, GTR was fully absorbed into the CNR on a date when all constituent companies were merged into the Crown corporation.

At the time that the GTR was fully merged into CNR, approximately 125 smaller railway companies comprised the Grand Trunk system, totalling 12,800 kilometres in Canada, and 1,873 kilometres in the U.S.