As a result of their promotion, Avispa Fukuoka would qualify in the 2016 J.League Cup. They were put in Group B alongside Yokohama F. Marinos, Kawasaki Frontale, Kashiwa Reysol, Vegalta Sendai, Albirex Niigata, and Sagan Tosu. Avispa Fukuoka recorded two wins and only one loss out of six matches, including a 1-0 away win versus Kawasaki Frontale and a 4-2 home win against Albirex Niigata, and thus qualified for the quarter-finals after finishing second on the table, much to the surprise of many as they were fighting in the relegation zone most of the time in their first season back in the top flight.
Avispa Fukuoka were seeded against fourth-place finisher FC Tokyo, and would play their games on 31 August and 4 September. They drew the first leg 1-1 at Ajinomoto Stadium in Chōfu, but could not get a win on their second leg as they lost 0-2 in Hakata-ku, Fukuoka.