He served as deputy governor of the Colony of Rhode Island and Providence Plantations.
He was the son of former Deputy Governor Jonathan Nichols Sr. and Elizabeth Lawton.
In 1755, Nichols was again selected as Deputy Governor, completing his first one-year term, then dying during his second year in office.
Following his death, the house was owned by Deputy Governor Joseph Wanton Jr., a loyalist, and following the American Revolutionary War was owned by William Hunter, a United States Senator, and ambassador to Brazil.
The ancestry of Jonathan Nichols Jr. is found in Austin's Genealogical Dictionary of Rhode Island.