Lushington was born into a gentry family, the son of a baronet, while his uncle was a judge and a member of parliament. Stephen entered the navy shortly after the end of the Napoleonic Wars, and after serving under a number of officers in far-flung locations like the Mediterranean and the South American coast, rose through the ranks. He was particularly active against pirates in the Aegean Sea and was promoted to lieutenant after a number of boat actions. He returned to the Mediterranean at his new rank and saw action at the Battle of Navarino, where the British were allied with the Russians against the Ottoman forces. Lushington came to the attention of Admiral Sir Edward Codrington, the British commander in chief, and was soon promoted to his own command, that of a bomb vessel. He distinguished himself while supporting French operations in the Morea expedition, and received French and Greek honours for his part in attack on an Ottoman position, as well as the professional approbation of the French naval commander.