At the age of 14, he was orphaned when his father Jeremiah, a 48-year-old miller, died in an accident at his mill. In his youth he ran a store in Moosup Valley.
In 1856 Phillips married his cousin Robie Alzada Place, a descendant of Anne Hutchinson and a devout member of the Rhode Island denomination of Baptists founded by Roger Williams. His children were eventually confirmed in Williams' church, the First Baptist Church in America.
He operated a successful sawmill in the village of Greene, named by him for another hero of the American Revolution, Nathanael Greene. From 1870-1872, he served in the Rhode Island House of Representatives. In 1874, he sold out and settled in Providence, where his family joined the ranks of society. He served in several public offices and joined every organization in Providence, including the Masons. He invented a fringe-trimming machine and made a good deal of money from it, at several points traveling to Europe.
With his wife he had five children,
- Lillian Delora Phillips (1856–1932)
- Sarah Susan Phillips (1857–1921) (mother of H. P. Lovecraft)
- Emeline Estella Phillips (1859–1865)
- Edwin Everett Phillips (1864–1918)
- Annie Emeline Phillips (1866–1941)
Whipple ran the successful Owyhee Land and Irrigation Company. In 1900, however, a dam built by his company on the Snake River in Idaho failed, as did a replacement dam. He was forced to sell off personal property to avoid complete ruin.
In his old age he helped raise the young H.P. Lovecraft and educated him not only in the classics, but also in original weird tales of "winged horrors" and "deep, low, moaning sounds" which he created for his grandchild's entertainment. The exact sources of Phillips' weird tales have not been identified. Lovecraft himself guessed that they originated from classic Gothic novelists like Ann Radcliffe, Matthew Lewis, and Charles Maturin, which were however not extant in the parts of Phillips' library bequeathed to Lovecraft.
On Sunday evening, March 27, 1904, while he was visiting the home of a crony, Alderman Gray, he was seized by a “paralytic shock,” likely a stroke. He died the following day, near midnight at his home at 454 Angell Street.