Bellingham is the homeland of Coast Salish peoples of the Lummi and neighboring tribes.

The first European immigrants reached the area about 1852 when Henry Roeder and Russel Peabody set up a lumber mill at Whatcom, now the northern part of Bellingham. Lumber cutting and milling continues to the present in Whatcom county. At about the same time, Dan Harris arrived, claiming a homestead along Padden Creek, and after acquiring surrounding properties, platted the town of Fairhaven in 1883. In 1858, the Fraser Canyon Gold Rush caused a short lived population growth that established the community. Coal was mined in the Bellingham Bay area from the mid-19th to the mid-20th centuries starting when Henry Roeder's agents discovered coal south of Whatcom Creek, in an area called Sehome, now downtown Bellingham, in 1854. They sold the coal baring land to San Francisco investors who established the Bellingham Bay Coal Company, eventually a subsidiary of the Black Diamond Coal Mining Company. After a hundred years of extensive mining beneath present-day Bellingham, the last mine closed in 1955.

In the early 1890s, three railroad lines arrived, connecting the bay cities to a nationwide market of builders. In 1889, Pierre Cornwall and an association of investors formed the Bellingham Bay Improvement Company (BBIC). The BBIC invested in several diverse enterprises such as shipping, coal, mining, railroad construction, real estate sales and utilities. Even though their dreams of turning the cities by the bay into a Pacific Northwest metropolis never came to fruition, the BBIC made an immense contribution to the economic development of Bellingham.

BBIC was not the only outside firm with an interest in the bay area utilities. The General Electric Company of New York purchased the Fairhaven Line and New Whatcom street rail line in 1897. In 1898, the utility merged into the Northern Railway and Improvement Company which prompted the Electric Corporation of Boston to purchase a large block of shares.

In 1890, Fairhaven developers bought the tiny community of Bellingham. Whatcom and Sehome merged in 1891 to form New Whatcom (1903 act of the State legislature dropped "New" from the name.) At first, attempts to combine Fairhaven and Whatcom failed, and there was controversy over the name of the proposed new city. Whatcom citizens would not support a city named Fairhaven, and Fairhaven residents would not support a city named Whatcom. They eventually settled on the name Bellingham, which remains today. Voting a second time for a final merger of Fairhaven and Whatcom into a single city, the resolution passed with 2163 votes for and 596 against.

Bellingham was officially incorporated on December 28, 1903, as a result of the incremental consolidation of the four towns initially situated on the east of Bellingham Bay during the final decade of the 19th Century. Whatcom is today's "Old Town" area and was founded with Roeder's Mill in 1852. Sehome was an area of downtown founded with the Sehome Coal Mine in 1854. Bellingham was further south near Boulevard Park, founded in 1883 and purchased in 1890 by Fairhaven. Fairhaven was a large commercial district with its own harbor, founded in 1883, by Dan Harris, around his initial homestead on Padden Creek.

Bellingham was the site of the Bellingham riots against East Indian (Sikh) immigrant workers in 1907. A mob of 400–500 white men, predominantly members of the Asiatic Exclusion League, with intentions to exclude East Indian immigrants from the work force of the local lumber mills, attacked the homes of the South Asian Indians. The Indians were mostly Sikhs but were labelled as Hindus by much of the media of the day.

Bellingham's proximity to the Strait of Juan de Fuca and to the Inside Passage to Alaska helped keep some cannery operations here. Pacific American Fisheries (P.A.F.), for example, shipped empty cans to Alaska, where they were packed with fish and shipped back.

As of 2000, the median income for a household in the city was $32,530, and the median income for a family was $47,196. Males had a median income of $35,288 versus $25,971 for females. The per capita income for the city was $19,483. About 9.4% of families and 20.6% of the population were below the poverty line, including 17.2% of those under age 18 and 9.0% of those aged 65 or over.

As of the census of 2010, there were 80,885 people, 34,671 households, and 16,129 families residing in the city. The population density was 2,986.9 inhabitants per square mile (1,153.2/km²). There were 36,760 housing units at an average density of 1,357.5 per square mile (524.1/km²). The racial makeup of the city was 84.9% White, 1.3% African American, 1.3% Native American, 5.1% Asian, 0.3% Pacific Islander, 2.8% from other races, and 4.3% from two or more races. Hispanic or Latino of any race were 7.0% of the population.

There were 34,671 households, of which 21.1% had children under the age of 18 living with them, 34.2% were married couples living together, 8.9% had a female householder with no husband present, 3.5% had a male householder with no wife present, and 53.5% were non-families. 35.3% of all households were made up of individuals, and 10.8% had someone living alone who was 65 years of age or older. The average household size was 2.18 and the average family size was 2.79.

The median age in the city was 31.3 years. 15.6% of residents were under the age of 18; 23.5% were between the ages of 18 and 24; 25.9% were from 25 to 44; 22% were from 45 to 64; and 12.8% were 65 years of age or older. The gender makeup of the city was 48.8% male and 51.2% female.