Mills scored 102 goals for Whitehawk after joining the club in 2012, having previously had spells with clubs including Peterborough and Torquay.
Details of the length of the 26-year-old's contract at Stonebridge Road have not been disclosed.
Mills is Ebbsfleet's first signing since winning promotion from National League South in May.
Newly-promoted National League side Ebbsfleet United have signed former Whitehawk striker Danny Mills.