Former Nuneaton Borough boss Eaden took replaced Marcus Law this summer but leaves the club having won twice in their opening 11 National League North games.
The Poppies were also dumped out of the FA Cup on Tuesday night, losing their Second Qualifying Round replay to Sutton Coldfield.
A statement on the club's official website read: "Kettering Town Football Club can confirm that first team manager Nicky Eaden has left the club with immediate effect.
"This decision has been made following our poor start to the league campaign and early exit from this year’s FA Cup. The board accept that the step up, to the National League structure, was always going to be challenging but recent performances and our FA Cup elimination were not acceptable.
"Steve Kinniburgh and Luke Graham will take the role of joint caretaker manager, while the club conducts a thorough recruitment process for a new, full-time manager."