It started on 31 August 2013 and ended on 1 January 2014 with the final at National Stadium in Tokyo.
The cup winners would normally receive a berth in the upcoming AFC Champions League; as F. Marinos finished as J.League runners-up that year, the nod went to Cerezo Osaka, the fourth-placed team in the 2013 J.League Division 1.
The 47 prefectural tournament winners join JFL seeded team Kamatamare Sanuki in the first round.
Nagano Parceiro and Zweigen Kanazawa, both playing in the Japan Football League, were the lowest-ranked teams remaining at this stage in the competition.
Only three teams outside the top flight remain: Consadole Sapporo and Montedio Yamagata of J.League Division 2 and Nagano Parceiro of the Japan Football League.