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The area is the home of the Tongva, Luiseño, and Juaneño tribal nations, who were there "as early as 4,000 years ago." The Tongva defined their world as Tovaangar, a nation which "extended from Palos Verdes to San Bernardino, from Saddleback Mountain to the San Fernando Valley" and included the entire territory of present-day Yorba Linda. Spanish colonization between 1769 and 1840 brought "disease, invasive species, and livestock" into the area, which "upended the ecological balance of the region and forced the Tongva to resettle around three missions."

In 1810, the Spanish crown granted José Antonio Yorba 63,414 acres of land, which "spread across much of modern-day Orange County." In 1834, following Mexico's independence from Spain, Yorba's most successful son, Bernardo Yorba (after whom the city would later be named), was granted the 13,328-acre (53.94 km²) Rancho Cañón de Santa Ana by Mexican governor José Figueroa. Most of this original land was retained after the Mexican–American War in 1848 by descendants of the Yorba family. A portion of the city's land is still owned and developed by descendants of Samuel Kraemer, who acquired it through his marriage to Angelina Yorba, the great-granddaughter of Bernardo Yorba. The site of the Bernardo Yorba Hacienda, referred to as the Don Bernardo Yorba Ranch House Site, is listed as a California Historical Landmark.

Near that same site sits the second oldest private cemetery in the county, the historic Yorba Cemetery. The land was given to the Roman Catholic Archdiocese of Los Angeles by Bernardo Yorba in 1858 since Orange County was not established out of Los Angeles County as a separate county until 1889. The cemetery closed in 1939 and was subsequently vandalized; however, in the 1960s, the Orange County Board of Supervisors took possession of the property to repair the damage, and tours are now available one day per month.

A section of the land was sold in 1907 by the Yorba family to Fullerton businessman Jacob Stern, who used the land for barley fields and sheep grazing. Stern subsequently sold the tract to the Janss Investment Company, which first called the area Yorba Linda, and proceeded to subdivide the land and sell it for agriculture and manufacturing. In 1910, the agricultural aspect of that endeavor materialized, and the first of many lemon and orange groves were planted: at the time, the population was still less than 50. A year later, The Pacific Telephone & Telegraph Company began serving Yorba Linda, and the first school was constructed.

In 1912, several things happened in Yorba Linda: it received its first post office; the Yorba Linda Citrus Association was founded; the Southern California Edison Company began providing electricity; and the first church was constructed. The area that would later become downtown was also connected to Los Angeles by the Pacific Electric Railway in 1912, primarily for citrus transport.

In 1913, Richard Nixon was born in Yorba Linda, the chamber of commerce was set up, a library opened as part of the school, and avocado trees were first planted. A year later, a separate district was established for the library system.

In 1915, the Susanna Bixby Bryant Ranch house was constructed. It is a museum that is open to the public.

In 1917, the first street was paved, Yorba Linda Boulevard. The Yorba Linda Star began publication also. It has since become an online section of the OC Register. A printed version of the Star is available at various city buildings free of charge and is delivered to every household in Yorba Linda each Thursday. Past articles are on microfilm at the Yorba Linda Public Library.

The population exceeded 300 for the first time prior to 1920. In 1929, the citrus association's packing house burned down, as it was made of wood. It reopened the next year. During this period, the eastern two-thirds of Yorba Linda (east of the Yorba Linda Country Club) remained part of cattle and agricultural ranches controlled by pioneer families such as the Yorba, de los Reyes, Kraemer, Travis, Dominguez, Friend, and Bryant ranches.

From 1943 to 1958, "approximately seventy thousand braceros were transported to Orange County," used by employers to service citrus crops. Braceros lived in temporary housing projects referred to as "camps," which were policed by local deputies throughout the county. The townspeople of Yorba Linda "refused to allow the housing of braceros in their city, forcing the nearby town of Placentia to board them within the segregated Mexican colonia."

The small town had grown significantly by the 1960s, with more than 1,000 residents by the 1960 Census. Three annexation attempts were made by adjoining cities: Brea in 1958 and Anaheim and Placentia in 1963. These experiences culminated in incorporation, which occurred in 1967.

The new city implemented a municipal general plan in 1972. By the 1980 Census, the population was nearing 30,000. Within ten years it exceeded 50,000.

In 1990, the Birthplace of Richard Nixon opened as a public library and museum. It would later become a federal presidential library. In 1994, the community center opened.

With over 20,000 housing units in the city as of 2016, many residents now oppose further urban development and have organized to reduce traffic congestion. The Yorba Linda Preservation Foundation seeks to protect historical buildings in the city.

In 2005, CNN ranked Yorba Linda as the 21st best place in the U.S. to live. In 2012, Yorba Linda was ranked 42nd on Money magazine's list of America's best small cities. Similarly, in an article by CNN Money, Yorba Linda was one of the richest U.S. cities and the richest in Orange County as reported by the Census data, showing a median household income of more than $120K: "Among towns of between 65,000 and 250,000 in population, Yorba Linda, California, where six-figure incomes are the rule, had the highest median income at $121,075". Yorba Linda has been identified as one of the richest cities in the U.S. by the U.S. Census Bureau, which shows a median household income of $121,075, higher than any other city in 2006.

In 2007, Yorba Linda High School broke ground after many years of planning.

In November 2008, eastern Yorba Linda suffered from fires that destroyed 113 homes and damaged 50 others. The destruction was due largely to erratic winds causing embers to fly up to half a mile away.

In 2012, an African American family who had moved to Yorba Linda in May 2011 reported to the Orange County Human Relations Commission that they had encountered numerous racially-motivated attacks, including rocks and acid pellets thrown towards their home, slashed tires, and their son was told by other children he could not play with them at Travis Ranch Elementary School because he was black. The family eventually moved to Corona in October of that year.

On February 3, 2019 at approximately 1:45 pm, a twin engine 1981 Cessna (N414RS) on route from Fullerton Municipal Airport to Nevada crashed from roughly 7500 ft into a single family residence in the 19700 block of Crestknoll Drive near Glenknoll Elementary School. The pilot (75-year-old Antonio Pastini) and four individuals in the residence were killed.

As of the 2000 Census, there were 58,918 people, 19,252 households, and 16,094 families residing in the city. The population density was 3,042.3 inhabitants per square mile (1,174.4/km²). There were 19,567 housing units at an average density of 1,010.4 per square mile (390.0/km²). The racial makeup of the city was 81.5% White, 1.2% African American, 0.4% Native American, 11.1% Asian, 0.1% Pacific Islander, 2.7% from other races, and 3.1% from two or more races. Hispanic or Latino of any race were 10.3% of the population.

There were 19,252 households, out of which 44.8% had children under the age of 18 living with them, 72.3% were married couples living together, 8.3% had a female householder with no husband present, and 16.4% were non-families. 12.4% of all households were made up of individuals, and 4.7% had someone living alone who was 65 years of age or older. The average household size was 3.05 and the average family size was 3.35.

In the city, the population was spread out, with 29.3% under the age of 18, 7.3% from 18 to 24, 28.4% from 25 to 44, 27.3% from 45 to 64, and 7.7% who were 65 years of age or older. The median age was 37 years. For every 100 females, there were 96.6 males. For every 100 females age 18 and over, there were 93.1 males.

According to a 2007 estimate, the median household income in the city was $109,681, and the median income for a family was $122,373. Males had a median income of $66,712 versus $41,820 for females. The per capita income for the city was $36,173. 0% of the population were below the poverty line.

The 2010 United States Census reported that Yorba Linda had a population of 65,237.

The population density was 3,208.8 people per square mile (1,238.9/km²).

The racial makeup of Yorba Linda was:

The Census reported that 64,044 people (99.7% of the population) lived in households, 97 (0.2%) lived in non-institutionalized group quarters, and 93 (0.1%) were institutionalized.

There were 21,576 households, out of which 8,535 (39.6%) had children under the age of 18 living in them, 15,102 (70.0%) were opposite-sex married couples living together, 1,844 (8.5%) had a female householder with no husband present, 758 (3.5%) had a male householder with no wife present. There were 554 (2.6%) unmarried opposite-sex partnerships, and 101 (0.5%) same-sex married couples or partnerships. 3,119 households (14.5%) were made up of individuals, and 1,515 (7.0%) had someone living alone who was 65 years of age or older. The average household size was 2.97. There were 17,704 families (82.1% of all households); the average family size was 3.29.

The population was spread out, with 15,792 people (24.6%) under the age of 18, 5,574 people (8.7%) aged 18 to 24, 13,848 people (21.6%) aged 25 to 44, 21,414 people (33.3%) aged 45 to 64, and 7,606 people (11.8%) who were 65 years of age or older. The median age was 41.7 years. For every 100 females, there were 94.8 males. For every 100 females age 18 and over, there were 92.2 males.

There were 22,305 housing units at an average density of 1,114.2 per square mile (430.2/km²), of which 18,108 (83.9%) were owner-occupied, and 3,468 (16.1%) were occupied by renters. The homeowner vacancy rate was 1.2%; the rental vacancy rate was 4.0%. 54,464 people (84.8% of the population) lived in owner-occupied housing units and 9,580 people (14.9%) lived in rental housing units.

During 2009–2013, Yorba Linda had a median household income of $112,259, with 3.1% of the population living below the federal poverty line.