He was second-in-command on HMS Sirius as second captain. The captain of that ship, Arthur Phillip, founded New South Wales. Hunter carried a dormant commission as successor to Phillip if he should die.
Hunter returned to England in 1792 after the loss of HMS Sirius. Whilst in England, Hunter saw service in the war with France. With Arthur Phillip's resignation from the governorship of New South Wales in 1793, Hunter was appointed governor and took up his appointment in 1795
Hunter's years as governor were difficult due to a power struggle between military and civil authorities in New South Wales. During the time between Phillip's departure and Hunter's arrival, the military took control of the colony and its institutions. These difficulties continued for the following governors Philip King and William Bligh and eventually resulted in the Rum Rebellion. Hunter is said to have been a compassionate governor.
Hunter died in England
The Hunter River and Hunter Valley north of Sydney are both named after him.