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The city was named after the nearby Weiser River, but exactly who that was named for is not precisely known. In one version it is for Peter M. Weiser, a soldier and member of the Lewis and Clark Expedition of 1804–1806. Another has it for Jacob Weiser, a trapper turned miner who struck it rich in Baboon Gulch in the Florence Basin of Idaho in 1861. William Logan and his wife Nancy were the first white settlers in the vicinity of Weiser in 1863 building a roadhouse in anticipation of the opening of Olds Ferry west of them on the Snake River across from Farewell Bend. In 1863, Reuben Olds acquired a franchise from the Territorial Legislature and began operating Olds Ferry. Olds ferry business did well (as did Logan's) as it diverted much of the traffic from the old Snake River crossing point at Old Fort Boise. Increasing settlement on the Weiser River valley increased Weiser's population. A post office was established in 1866 as Weiser Ranch. In 1871, it was renamed Weiser. Weiser reached its height of prosperity when a railroad way station was established and it became a transportation hub for travelers. Its history is well represented by the great number of original buildings from the 1890s and early 1900s that are on the National Register of Historic Places. During the 1890s, the city had pretensions of becoming a major regional market and transportation center. The Idaho Northern Railroad was built up the Weiser River with the intention of reaching Lewiston and river transportation to the ocean. The dream ended among the lumber mills of central Idaho almost at the community of Meadows not needing to actually go past the stock loading and lumber ponds outside the village, the terminus station was built there and a new city, New Meadows, came into being. Likewise the Union Pacific, after taking over the Oregon Short Line chose not to locate its major section yards in the flats west of Weiser—probably due to inflated prices asked by land speculators—and built at Huntington, Oregon at the western edge of the Snake River valley. Hall of Fame pitcher Walter Johnson played semi pro baseball for the Weiser Kids as a young man in 1906–1907. After high school in Fullerton, California, the "Big Train" was lured to Weiser to play baseball and work for the local telephone company. While in Weiser, he once pitched 84 consecutive scoreless innings. His skills drew the attention of the Washington Nationals, who sent scout Cliff Blankenship to offer Johnson a contract, and in July 1907 he departed Idaho for the major leagues at age nineteen. U. S. Route 95 runs through the city, connecting to Oregon and British Columbia.

Weiser bills itself as the "Fiddling Capital of the World" and the National Oldtime Fiddlers' Contest has been held each year since 1953. Fiddling contests have been held in Weiser since 1914, but the present festival was the idea of Blaine Stubblefield, a fiddler and folk music collector, and the head of the city's chamber of commerce. The festival is held at the beginning of summer, during the third full week in June, the only exception occurring during leap years when it is held on the 4th week of the month. It draws national media coverage and over 7,000 people to the Weiser area. The city has been consistently served by the Weiser Signal American, the local weekly newspaper. For many years Weiser's location as the last city upriver from Hells Canyon made it the jump off point for wilderness tours by powered rubber raft down the gorge. Enormous sturgeon and plentiful salmon were a draw for anglers. The salmon runs ended not long after the float tours with the blocking of the river by three hydro power dams built by Idaho Power Company starting in the 1950s.

Weiser is located at (44.249712, 116.967799), at an elevation of 2129 feet (649 m) above sea level. According to the United States Census Bureau, the city has a total area of 3.38 square miles (9 km2), all of it land. Unincorporated Annex, Oregon, sits across the Snake River.

Weiser experiences a semi arid climate (Köppen BSk) with cold winters and hot, dry summers.

employment at the hospital and school system includes jobs which have university education as a prerequisite, but not many other jobs in Weiser have that requirement.

Note: the US Census treats Hispanic/Latino as an ethnic category. This table excludes Latinos from the racial categories and assigns them to a separate category. Hispanics/Latinos can be of any race. +Weiser racial composition (NH = Non Hispanic)RaceNumberPercentageWhite (NH)3,80467.57%Black or African American (NH)90.16%Native American or Alaska Native (NH)470.83%Asian (NH)510.91%Pacific Islander (NH)30.05%Some Other Race (NH)260.46%Mixed/Multi Racial (NH)2694.78%Hispanic or Latino1,42125.24%Total5,630
As of the 2020 United States census, there were 5,630 people, 2,101 households, and 1,349 families residing in the city.

As of the census of 2010, there were 5,507 people, 2,158 households, and 1,396 families residing in the city. The population density was There were 2,355 housing units at an average density of The racial makeup of the city was 80.8% White, 0.3% African American, 0.9% Native American, 1.0% Asian, 14.3% from other races, and 2.7% from two or more races. Hispanic or Latino of any race were 26.1% of the population. There were 2,158 households, of which 33.4% had children under the age of 18 living with them, 46.2% were married couples living together, 13.2% had a female householder with no husband present, 5.3% had a male householder with no wife present, and 35.3% were non families. 30.2% of all households were made up of individuals, and 15.6% had someone living alone who was 65 years of age or older. The average household size was 2.50 and the average family size was 3.11. The median age in the city was 38.7 years. 26.4% of residents were under the age of 18; 7.8% were between the ages of 18 and 24; 22.7% were from 25 to 44; 24.3% were from 45 to 64; and 18.7% were 65 years of age or older. The gender makeup of the city was 48.4% male and 51.6% female.

As of the census of 2000, there were 5,343 people, 2,018 households, and 1,368 families residing in the city. The population density was There were 2,207 housing units at an average density of The racial makeup of the city was 81.13% White, 0.07% African American, 0.80% Native American, 1.20% Asian, 0.13% Pacific Islander, 13.92% from other races, and 2.73% from two or more races. Hispanic or Latino of any race were 22.91% of the population. There were 2,018 households, out of which 33.4% had children under the age of 18 living with them, 52.4% were married couples living together, 11.2% had a female householder with no husband present, and 32.2% were non families. 28.0% of all households were made up of individuals, and 17.0% had someone living alone who was 65 years of age or older. The average household size was 2.58 and the average family size was 3.19. In the city, the age distribution of the population shows 28.3% under the age of 18, 9.2% from 18 to 24, 24.1% from 25 to 44, 19.9% from 45 to 64, and 18.5% who were 65 years of age or older. The median age was 36 years. For every 100 females, there were 90.8 males. For every 100 females age 18 and over, there were 86.6 males. The median income for a household in the city was $26,880, and the median income for a family was $31,996. Males had a median income of $26,643 versus $16,386 for females. The per capita income for the city was $13,986. About 12.6% of families and 15.4% of the population were below the poverty line, including 17.9% of those under age 18 and 10.8% of those age 65 or over.

It is in the Weiser School District 431. The Weiser school district consists of Pioneer Elementary School, Kindergarten, 1st, 2nd, and 3rd grades , Park Intermediate School, 4th and 5th grade, Weiser Middle School, 6th, 7th, and 8th grade, and Weiser High School, 9th, 10th, 11th, and 12th grades. The first school in Weiser was established in 1867, and the first school building was built in 1882. A dedicated building for the high school opened in 1904. During or after the 1890s Weiser Academy a. k. a. Intermountain Institute, a boarding school, was established by a preacher named Edward Paddock. The National Youth Administration (NYA) took a part of the boarding school facility in the 1930s after Paddock experienced old age and ill health. In 1948 the whole boarding school property was given to the high school. Washington County is in the area (but not the taxing region) of the College of Western Idaho, which has its main campus in Nampa.