Stopford became Rear-Admiral of the United Kingdom in 1834. His last active post, in his early seventies, was as commander-in-chief of the Mediterranean fleet during the Syrian War against the forces of Mehemet Ali. As Vice Admiral on board (100) and subsequently , he was in command of the combined British, Turkish, and Austrian fleet during the bombardment of Acre on 3 November 1840. For his services in the Syrian War, Stopford was given the Freedom of the City of the City of London and presented with a commemorative "freedom box". The ornate silver and oak box is part of the collection of the National Maritime Museum, Greenwich. The following year he became Governor of the Greenwich Hospital at Greenwich, with the rank of admiral.