Khagan or Qaghan is a title of imperial rank in the Turkic, Mongolic and some other languages, equal to the status of emperor and someone who rules a khaganate (empire). The female equivalent is Khatun.

It may also be translated as "Khan of Khans", equivalent to King of Kings.

Since the division of the Mongol Empire, emperors of the Yuan dynasty held the title of Khagan and their successors in Mongolia continued to have the title.

"The Secret History of the Mongols", written for that very dynasty, clearly distinguishes Khagan and Khan: only Genghis Khan and his ruling descendants are called Khagan, while other rulers are referred to as Khan. The title "Khagan" or "Khaan" most literally translates to "great/supreme ruler" in the Mongol language, and by extension "sovereign", "monarch", "high king", or "emperor".

The title can also be expanded with the addition of "Yekhe" (meaning "great" or "grand") to produce "Yekhe Khagan", meaning "Great Emperor".

More Info: en.wikipedia.org