Brannan was born in Saco, Maine. As a teenager, his family moved to Ohio, where Brannan converted to the Church of Jesus Christ of Latter-day Saints (LDS Church) and learned to be a printer. He moved to New York in 1844, and began printing The New York Messenger, a Latter-day Saint (LDS; see also Mormon) newspaper.
On February 4, 1846, Brannan and about 240 other LDS from New York and set sail aboard the ship Brooklyn for California, via Cape Horn. They landed at Yerba Buena (now San Francisco) on July 31, 1846, tripling the size of the village. Brannan establised the first newspaper in San Francisco, the California Star. In 1847, he opened a store at Sutter's Fort, in what is now Sacramento. Early in 1848, employees of John Sutter paid for goods in his store with gold they had found at Sutter's Mill, near Coloma, California. Brannan went to the mill and, as a representative of the LDS Church, he received the tithes of the LDS workers there from the gold they had found in their spare time. Brannan took this gold back to San Francisco, proclaiming, "Gold, gold from the American River!"
Brannan opened more stores to sell goods to the miners (his Sutter Fort store sold $150,000 a month in 1849), and began buying land in San Francisco. At about this time, Brannan was excommunicated from the LDS Church for diverting church money to fund his private ventures. He was elected to the first town council for San Francisco, and was the orginizer of the Committee of Vigilance, which functioned as a de facto police force.
In 1851, Brannon visited Hawaii, and purchesed large amounts of land in Honolulu. In 1853 he was elected to the California Senate. In 1868 he purhcased 160,000 acres of land in Los Angeles County, California. His fortune dwindled late in life after failed land speculation with the Mexican government near Sonora Brannan died pennyless in San Diego, California on May 14, 1889, after suffering from bowel inflammation.