Thomas Whaley (October 5, 1823 – December 14, 1890) was an early settler of San Diego, California.

He was advised to go to San Diego, so he and Lewis Franklin sailed there in 1851 and opened a store called Tienda California.

They had six children, including Anna Amelia, George Hay Ringgold, Violet Eloise, and Corinne Lillian.

Whaley was appointed president of the San Diego board of trustees (informally called "mayor") during 1858–1859.

[1] In 1857, Thomas Whaley built a house in San Diego, in the area now referred to as Old Town.