He was born in Albany, New York, on August 25, 1836. He was named Francis Brett Hart after his great-grandfather Francis Brett. When he was young his father changed the spelling of the family name from Hart to Harte. Later, Francis preferred to be known by his middle name, but he spelled it with only one "t", becoming Bret Harte.

An avid reader as a boy, Harte published his first work at age 11, a satirical poem titled "Autumn Musings," now lost. His formal schooling ended when he was 13 in 1849. He moved to California in 1853, later working there in a number of capacities, including miner, teacher, messenger, and journalist. He spent part of his life in the northern California coastal town of Union (now known as Arcata), a settlement on Humboldt Bay that was established as a provisioning center for mining camps in the interior.

The 1860 massacre of between 80 and 200 Wiyots killed at the village of Tutulwat was well documented historically and was reported in San Francisco and New York by Harte. When serving as assistant editor for the Northern Californian, Harte editorialized about the slayings while his boss, Stephen G. Whipple, was temporarily absent, leaving Harte in charge of the paper. Harte published a detailed account condemning the event, writing, "a more shocking and revolting spectacle never was exhibited to the eyes of a Christian and civilized people. Old women wrinkled and decrepit lay weltering in blood, their brains dashed out and dabbled with their long grey hair. Infants scarcely a span long, with their faces cloven with hatchets and their bodies ghastly with wounds." After publishing the editorial, his life was threatened and he was forced to flee one month later. Harte quit his job and moved to San Francisco, where an anonymous letter published in a city paper is attributed to him, describing widespread community approval of the massacre. In addition, no one was ever brought to trial, despite the evidence of a planned attack and references to specific individuals, including a rancher named Larabee and other members of the unofficial militia called the Humboldt Volunteers.

Harte married Anna Griswold on August 11, 1862, in San Rafael, California. From the start, the marriage was rocky. Some suggested she was handicapped by extreme jealousy while an early biographer of Harte, Henry C. Merwin, privately concluded that she was "almost impossible to live with".

His first literary efforts, including poetry and prose, appeared in The Californian, an early literary journal edited by Charles Henry Webb. In 1868 he became editor of The Overland Monthly, another new literary magazine, but this one more in tune with the pioneering spirit of excitement in California. His story, "The Luck of Roaring Camp", appeared in the magazine's second issue, propelling Harte to nationwide fame.

When word of Charles Dickens's death reached Bret Harte in July 1870, he immediately sent a dispatch across the bay to San Francisco to hold back the forthcoming publication of his Overland Monthly for twenty-four hours, so that he could compose the poetic tribute, "Dickens in Camp". This work is considered by many of Harte's admirers as his verse masterpiece, for its evident sincerity, the depth of feeling it displays, and the unusual quality of its poetic expression.

Determined to pursue his literary career, in 1871 he and his family traveled back East, to New York and eventually to Boston, where he contracted with the publisher of The Atlantic Monthly for an annual salary of $10,000, "an unprecedented sum at the time." His popularity waned, however, and by the end of 1872 he was without a publishing contract and increasingly desperate. He spent the next few years struggling to publish new work (or republish old), delivering lectures about the gold rush, and even selling an advertising jingle to a soap company.

In 1878 Harte was appointed to the position of United States Consul in the town of Krefeld, Germany, and then to Glasgow in 1880. In 1885 he settled in London. During the twenty-four years he spent in Europe, he never abandoned writing, and maintained a prodigious output of stories that retained the freshness of his earlier work. He died in England in 1902 of throat cancer and is buried at Frimley.

His wife, by then known as Anna Bret Harte, died on August 2, 1920. Despite being married for nearly forty years, the couple lived together for only sixteen of those years.

In his Round the World, Andrew Carnegie praised Bret Harte as uniquely American:

A whispering pine of the Sierras transplanted to Fifth Avenue! How could it grow? Although it shows some faint signs of life, how sickly are the leaves! As for fruit, there is none. America had in Bret Harte its most distinctively national poet.

Writing in his autobiography four years after Harte's death, however, Mark Twain characterized him and his writing as insincere. He criticized the miners' dialect used by Harte, claiming it never existed outside of his imagination. Twain accused Harte of borrowing money from his friends with no intent to repay and of financially abandoning his wife and children.