He was given command of Massachusetts ship Winthrop which captured two British privateers, armed brig Meriam, and a number of other vessels.
The next year saw a second cruise, which culminated with the capture of the French corvette Le Berceau and seven other ships.
On their return, Little found himself in the middle of a political firestorm, the capture of Le Berceau having taken place two weeks after the signing of the Treaty of Mortefontaine had ended the Quasi-War.
Little also fought in court over an agreement with Silas Talbot to split the prize money for Les Deux Anges, taken by the Boston in January 1800.
This case, Talbot v. Little, also reached the Supreme Court, but was eventually dismissed without hearing, leaving Little and his crew the victors.