It was led by U.S. Army Brevet Lieutenant Colonel John C. Frémont and composed of his cartographers, scouts and hunters and the California Volunteer Militia formed after the Bear Flag Revolt.

The battalion's formation was officially authorized by Commodore Robert F. Stockton, commanding officer of the U.S. Navy Pacific Squadron.

In 1846, U.S. Marine Lieutenant Archibald H. Gillespie was sent by President James K. Polk with secret verbal messages to the U.S. Consul Thomas O. Larkin in Alta California's Capital in Monterey, Commodore John D. Sloat commanding the Pacific Squadron and U.S. Army Captain John C. Frémont doing cartography work in California.

A compact was drawn in early July 1846 for all volunteers to sign, which in part read: "Not to violate the chastity of Women; conduct their revolution honorably; and pledge obedience to their officers."

On 26 July 1846 Lt. Col. J. C. Frémont's California Battalion of about 160 boarded the sloop USS Cyane, under the command of Captain Samuel Francis Du Pont, and sailed for San Diego.

Leaving about 40 men to garrison San Diego, Frémont continued on to Los Angeles where on 13 August, with the Navy band playing and colors flying, the combined forces of Stockton and Frémont entered Pueblo de Los Angeles, without a man killed nor shot fired.

In Pueblo de Los Angeles, the largest city in California with about 3,000 residents, things might have remained peaceful, except that Major Gillespie placed the town under martial law, greatly angering some of the Californios.

On 23 September 1846, about 200-300 Californios under Gen. José María Flores staged a revolt, the Siege of Los Angeles, and exchanged shots with the Americans in their quarters at the Government House.

An American scouting party was attacked by a force of mounted Californios on the Rancho La Natividad in the Salinas Valley.

Frémont led his unit over the Santa Ynez Mountains at San Marcos Pass, in a rainstorm on the night of 24 December 1846.

In spite of losing many of his horses, mules, and cannon, which slid down the muddy slopes during the rainy night, his men regrouped in the foothills the next morning, and recaptured the Presidio without bloodshed.

Stockton and Kearny by ship went to San Diego and from there marched on Los Angeles with a combined force of about 500 sailors, marines and Army Dragoons.

A few days later Fremont led his men southeast towards Los Angeles, accepting the surrender of Andrés Pico on the Cahuenga Plain on 13 January 1847.

Frémont specifically quoted his title as California Battalion commander in the Treaty of Cahuenga: To All Who These Presents Shall Come, Greeting: Know Ye, that in consequence of propositions of peace, or cessation of hostilities, being submitted to me, as Commandant of the California Battalion of the United States forces, which have so far been acceded to by me as to cause me to appoint a board of commissioners to confer with a similar board appointed by the Californians, and it requiring a little time to close the negotiations; it is agreed upon and ordered by me that an entire cessation of hostilities shall take place until to-morrow afternoon (13 January), and that the said Californians be permitted to bring in their wounded to the mission of San Fernando, where, also, if they choose, they can move their camp to facilitate said negotiations.

As Kearny's forces steadily built up with the arrival of Colonel Jonathan D. Stevenson and his about 600 men in the 1st Regiment of New York Volunteers in March 1847 along with the departure of Commodore Robert Stockton left Frémont with almost no supporters.

Polk quickly commuted Frémont's sentence of dishonorable discharge in light of his service in the war and offered him reinstatement of his army commission.

Frémont however, considered his conviction an injustice and resigned his commission and moved back to California with his family settling on Rancho Las Mariposas that Thomas O. Larkin had bought for him at his request.