The Theosophist, Charles Leadbeater, alleged that the Secret Chief or “the Head of all true Freemasons” is Francis Bacon, 1st Viscount St Alban. (Note the use of the present tense despite the fact that Bacon is popularly believed to have died in 1626).
Some Memphis-Misraim rites believe that the Secret Chief of Freemasonry is a character named “Elias Artista,” whom Paracelsus first described as a sort of mythical patron saint of Alchemy. There are probably people who believe that Francis Bacon and Elias Artista are the same person.
Of course, whether you chose to believe this is another matter. Most Worshipful Brother Bacon has requested his name not be disclosed, so all true Freemasons will deny the existence of a Secret Chief of Freemasonry – as witness the other answers to this question.