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The recorded history of the Fremont area began on June 6, 1795, when Mission San José was founded by the Spaniard Father Fermin de Lasuen. The Mission was established at the site of the Ohlone village of Oroysom. On their second day in the area, the Mission party killed a grizzly bear in Niles Canyon. The first English-speaking visitor to Fremont was the renowned trapper and explorer Jedediah Smith in 1827. The Mission prospered, eventually reaching a population of 1,887 inhabitants in 1831. The influence of the missionaries declined after 1834, when the Mexican government enacted secularization.

José de Jesus Vallejo, brother of Mariano Vallejo, was the grantee of the Rancho Arroyo de la Alameda Mexican land grant. His family was influential in the Fremont area in the late colonial era and owned and built a flour mill at the mouth of Niles Canyon. In 1846 the town's namesake John C. Frémont led a military expedition to map a trail through Mission Pass for reaching the Pacific coast and to take possession of California from Mexico for the United States.

The Fremont area grew rapidly at the time of the California Gold Rush. A town called Mission San José grew up around the old mission, with its own post office from 1850. Agriculture dominated the economy with grapes, nursery plants and olives as leading crops. In 1868 the 6.8-magnitude Hayward earthquake on the Hayward Fault collapsed buildings throughout the Fremont area, ruining Mission San José and its outbuildings. Until the 1906 San Francisco earthquake caused its destruction, the Fremont area's Palmdale Winery was the largest in California. The ruins of the Palmdale Winery are still visible near the Five Corners in Irvington.

From 1912 to 1915, the Niles section of the Fremont area was the earliest home of California's motion picture industry (see Essanay Studios). Charlie Chaplin filmed several movies in the Fremont area, most notably The Tramp.

Fremont was incorporated in 1956 under the leadership of Wally Pond, chair of the incorporation committee, when five towns in the area, Irvington, Centerville, Mission San José, Niles, and Warm Springs, came together to form a city. Glenmoor Gardens, the largest subdivision in Fremont, was under construction in the area, by developers Ralph E. Cotter, Jr., James R. Meyer, civil engineer Fred T. Duvall, and contractors James L. Reeder, and Robert H. Reeder. When the Glenmoor Gardens Homeowners Association (GGHA) was incorporated, in March 1953, there were no more than 75 houses in the subdivision. It was probably the first such organization in the Fremont area; in its scope and structure. The five-member board of directors (which included James Meyer and James Reeder) was set up to oversee a full range of services, from police and fire protection to street maintenance (which later became the purview of the city government).

Fremont became more industrialized between 1953 and 1962. A boom in high-tech employment in the 1980s to the late 1990s, especially in the Warm Springs District, caused rapid development in the city and linked the city with the Silicon Valley. The Apple factory where the first Mac computer was manufactured was located in Fremont; production ceased in 1993. Other semiconductor and telecommunications firms soon opened in the city, including Cirrus Logic, Asyst Technologies, Mattson Technology, Lam Research, Premisys Communications, and Nextlink California. Approximately 750 high tech companies had offices, headquarters or production facilities in Fremont by 1999. These firms included fifteen of the top one hundred fastest-growing public companies in the San Francisco Bay Area and eighteen of the top fifty companies in the East Bay. The high-tech growth in Fremont continues today and is a major industry for the city.

The General Motors automotive assembly plant in South Fremont was the town's largest employer, and Fremont was known for its drag strip. In the 1980s, the plant became a joint venture automotive assembly plant of Toyota and General Motors, and was renamed NUMMI. Toyota and NUMMI shut down its operations in early 2010. Part of the plant was acquired in June 2010 by Tesla Motors as its primary production plant, known as the Tesla Factory.

Solyndra, a solar panel manufacturer, was personally promoted in 2010 by President Barack Obama as a model for government investment in green technology after his administration approved a $535-million Department of Energy loan guarantee and the company built a $733 million state-of-the-art robotic facility, but in 2011 the company filed for Chapter 11 bankruptcy and laid-off 1,000 workers. Data storage company Seagate Technology, incorporated in the Republic of Ireland with executive offices in Cupertino, acquired the former Solyndra building.

The first Fremont post office opened in 1956.

According to a 2018 estimate, the median income for a household in the city is $122,191, and the median income for a family was $103,846. Males have a median household income of $59,274 versus $40,625 for females. The per capita income for the city was $31,411. About 3.6% of families and 5.4% of the population were below the poverty line, including 5.9% of those under age 18 and 6.2% of those age 65 or over.

The 2010 United States Census reported that Fremont had a population of 214,089. The population density was 2,443.7 people per square mile (943.5/km²).

The Census reported that 212,438 people (99.2% of the population) lived in households, 969 (0.5%) lived in non-institutionalized group quarters, and 682 (0.3%) were institutionalized.

There were 71,004 households, out of which 31,070 (43.8%) had children under the age of 18 living in them, 45,121 (63.5%) were opposite-sex married couples living together, 7,070 (10.0%) had a female householder with no husband present, 3,382 (4.8%) had a male householder with no wife present. There were 2,779 (3.9%) unmarried opposite-sex partnerships, and 444 (0.6%) same-sex married couples or partnerships. 11,576 households (16.3%) were made up of individuals, and 3,697 (5.2%) had someone living alone who was 65 years of age or older. The average household size was 2.99. There were 55,573 families (78.3% of all households); the average family size was 3.36.

The population was spread out, with 53,216 people (24.9%) under the age of 18, 15,610 people (7.3%) aged 18 to 24, 66,944 people (31.3%) aged 25 to 44, 56,510 people (26.4%) aged 45 to 64, and 21,809 people (10.2%) who were 65 years of age or older. The median age was 36.8 years. For every 100 females, there were 98.9 males. For every 100 females age 18 and over, there were 96.4 males.

There were 73,989 housing units at an average density of 844.5 per square mile (326.1/km²), of which 71,004 were occupied, of which 44,463 (62.6%) were owner-occupied, and 26,541 (37.4%) were occupied by renters. The homeowner vacancy rate was 1.3%; the rental vacancy rate was 4.5%. 136,606 people (63.8% of the population) lived in owner-occupied housing units and 75,832 people (35.4%) lived in rental housing units.

Fremont has a large Deaf community, in large part because it is home of the Northern California campus of the California School for the Deaf. The school district is called the Fremont Unified School District which also serves parts of Union City and Hayward.

As of 2010 more than half the residents of Fremont were of Asian ancestry, with large populations of Chinese, Asian Indians, and Filipinos.

The racial makeup of Fremont was:

108,332 (50.6%) Asian (consisting of 18.1% Indian, 17.8% Chinese, 6.7% Filipino, 2.5% Vietnamese, 1.8% Korean, 1.0% Pakistani, 0.8% Japanese, 0.6% Burmese)
70,320 (32.8%) White, Non-Hispanic Whites were 26.5% of the population in 2010, down from 85.4% in 1970.)
31,698 (14.8%) Hispanic or Latino of any race. (consisting of 11.0% Mexican, 0.6% Puerto Rican, 0.5% Salvadoran).
13,605 (6.4%) from other races,
12,584 (5.9%) from two or more races
7,103 (3.3%) African American,
1,169 (0.5%) Pacific Islander,
976 (0.5%) Native American,

Due in large part to a substantial influx of Afghans granted asylum in the United States following the 1979 invasion of Afghanistan by the Soviet Union, Fremont is the home to the largest concentration of Afghan Americans in the United States. This is noted in Khaled Hosseini's 2003 novel Kite Runner.

Fremont and nearby Union City have fairly large numbers of Pacific Islanders, Cubans and Puerto Ricans, Spanish and Portuguese, and a small number of American Indians.