[3][4][5] In the 1989–90 Greek League Cup, the participants were the 18 teams of the 1989–90 Alpha Ethniki.
If the score was level at the end of normal time, extra time was played, followed by a penalty shoot-out if the score was still level.
The team that scored more goals on aggregate over the two legs advanced to the next round.
If the aggregate score was level, the away goals rule was applied, i.e. the team that scored more goals away from home over the two legs advanced.
If no goals were scored during extra time, the winners were decided by a penalty shoot-out.