On Jan. 21, 1895, the Alaska Steamship Company was finalized. The first vessel purchased was the 140-foot steamer WILLAPA.

Sustaining the company's growth was the completion of a railroad into the interior, encouraging mining activity for precious metals that brought both fortune-seekers and tourists. By 1905, activity shifted from the Juneau/Skagway area to Valdez/Cordova, then eventually to Nome, where Alaska Steamship was ready to capitalize on the bonanza by switching its ships accordingly. At the end of 1897, Charles Peabody reorganized the Alaska Steamship Co. and his fleet expanded rapidly as the Klondike gold stampede mounted. In 1898 the stockholders formed the Puget Sound Navigation Co. as an inland water subsidiary. That new company was registered in Nevada where corporate laws were more lenient. The Puget Sound routes were a natural place for the company to recycle some of its smaller original vessels as they became obsolete for the strenuous Alaska runs.

As the turn of the century was approaching, several events were causing tremendous increases in Southeast Alaskan marine travel: religious missions were being established, fish canneries were being built and gold had been discovered. The Inside Passage was a major route to overland staging areas for the gold fields.

In 1902, Peabody and his associates initiated through Puget Sound Navigation Co. a Port Townsend and Port Angeles to Victoria steamship route for both freight and passengers. Pacific Steamship Co. was caught napping as they had committed all their ships to the Klondike run, which was still running as the gold rush slowly subsided. The other possible competitor, Canadian Pacific Railway, initially declined to compete on the route, concentrating instead on their Empress ocean going sleek steamships that connected with their rail route across the Canadian Rockies and their Empress Hotels in Victoria and Vancouver. On May 2, 1903, the Alaska Steamship Co., purchased the controlling stock of La Conner Trading & Transportation Co. The new concern was initially named Inland Navigation Co. but as Puget Sound Navigation Co., the resulting company would become the biggest inland shipping company of Puget Sound. Charles Peabody controlled the majority of stock and he became president of the enlarged company. Soon afterwards, Peabody became chairman of the board.

In 1909, a group known as the Alaska Syndicate, with funds from J.P. Morgan and the Guggenheim Family Company, bought the Alaska Steamship Company so they could mine copper in the Wrangell Mountains. They merged the company with the Northwestern Steamship Co. Limited , keeping the Alaska Steamship Company name. The merger of the two companies just about gave them a monopoly in the Alaska shipping industry. They expanded the fleet into 18 ships and expanded service in Alaska from Ketchikan to Kotzebue. In 1912 Charles Peabody retired from Alaska Steamship Company and was replaced by S.W. Eccles of the Guggenheim Company. In 1915, Kennecott, Alaska Copper Company was formed and began acquiring stock from the Alaska Steamship Company.

The Jones Act, passed by Congress in 1920, known as the Merchant Marine Act, helped the Alaska Steamship and the Pacific Steamship companies. The law prohibited shipping between any two United States ports in anything but American-built ships. Two Canadian shipping companies serving Southeast Alaska communities were forced out of the Alaska market. In the 1930s Alaska Steam purchased is long time rival, the Pacific Steamship Company. Responding to Alaskans complaints about irregular service and high rates, Congress passed the Intercoastal Shipping Act in 1933. It called for definite shipping schedules and approved, published cargo rates.

At the outbreak of the Second World War, Alaska Steamship had a fleet of 16 vessels operating out of Seattle to Skagway, Seward and Nome. During World War II, the federal government took control of most U.S. registered ships for the war effort, including the ships of the Alaska Steamship Company and the company became an agent for the War Administration, was assigned its own ships and was given sixty others to manage.

It returned to peacetime operations under the ownership of Skinner and Eddy Corporation, Seattle, which purchased the Alaska Steamship in August 1944 for $4,290,000. During World War 2 five ships were lost.

After the war, the Alaska shipping industry changed. Only two major companies, Alaska Steamship Company and Northland Transportation Company served Alaska, both owned by the Skinner and Eddy Corporation in Washington. Before the war, 42 ships served Alaska; in 1948 only seven. The change was due to the end of federal subsidies, rising labour costs, and new competition from truckers and air carriers. The Alaska Steamship Company started to use tugs and barges and container ships. Tugs and barges could travel faster and operated with smaller crews 5 to 7 workers as compared to 30 to 40 on freighters. Containers could be trucked, lifted on and off, and trucked away, allowing faster loading.

The first passenger sailing out of Seattle was undertaken by ALASKA in January 1946. She was subsequently followed by the YUKON, ALEUTIAN, BARANOF and DENALI. Ports of call northbound were Ketchikan (two days), Juneau (three days) and Seward (five days), with occasional calls at Wrangell, Petersburg, Skagway, Sitka, Cordova, Valdez, Kodiak and Seldovia. Southbound, the steamers called at the same ports they stopped at heading north. All steamers had accommodation for over 200 passengers ranging from steerage to a deluxe cabin with private bath. It was during this period that the company decided to concentrate on tourism.

The Inside Passage to Alaska was a hazardous journey and Alaska Steamship was no stranger to its perils. On 4 February 1946 at 4 am during a blinding snowstorm and strong north easterly winds the YUKON ran aground near Cape Fairfield. Heavy seas prevented the launching of boats until daylight, by which time rescue vessels arrived to take off the frightened passengers and crew. Some years later another calamity was the collision of BARANOF with the Greek steamer Triton on 26 July 1952 near Nanaimo with the loss of two of the crew of the latter.

Many factors contributed to Alaska Steamship's eventual termination of passenger service. Firstly, there were continued labor problems caused by longshoremen, seamen and stewards. Secondly, the arrival of an air service (partly subsidized by the Government) to Alaska took away potential passengers and freight bookings and thirdly was the end of charter privileges and subsidy payments. The Alaska Steamship Company was facing insurmountable financial difficulties that even a new fleet of steamers could not remedy.

On 6 July 1954 therefore Mr. D.E. Skinner the president of Alaska Steamship Company announced that his firm was moving out of the passenger business. The BARANOF was immediately laid up, the ALASKA sailed until August, the DENALI made the company’s last passenger sailing in September 1954, The ships were then sold off.

The Alaska Steamship Company now concentrated on the carriage of cargo but declining revenues, rising operation costs forced the Company to shut down in January 1971.