The flag consisted of a Blue Ensign with the coat of arms of the predecessor state, the Septinsular Republic on it with a red border.

[1] In article 1 of section VI in the treaty, it stated that the new United States of the Ionian Islands' national flag would be the flag of the Septinsular Republic, a Lion of Saint Mark holding a Bible on a blue background, with a Union Jack in the canton to symbolise the British protectorate.

[3] During the Crimean War, ships flying the Ionian Islands flag were presumed to not be allowed to trade with Russia.

However the Judicial Committee of the Privy Council from the Admiralty court in 1855 held that as Queen Victoria had negotiated treaties with other nations specifically including the United States of the Ionian Islands separately, instead of the implied inclusion with the Crown Colonies through mentioning just the United Kingdom alone, the Ionian Islands were not technically at war with the Russian Empire as the United Kingdom had not separately declared war on their behalf by mentioning them in the original declaration.

[4] In 1864, pursuant to the Treaty of London the United Kingdom ceded the United States of the Ionian Islands to the Kingdom of Greece as a gesture of goodwill following Prince Alfred declining to accept the Greek throne despite Greek popular request.