The 2006–07 Greek Football Cup was the 65th edition of the Greek Football Cup, competition. That season's edition was the first to be entitled "Hellas On Line Greek Cup". The competition started on 26 August 2006 and concluded on 5 May 2007 with the Final, held at the Panthessaliko Stadium. AEL won the trophy with a 2–1 victory over Panathinaikos.

Calendar

Knockout phase

Each tie in the knockout phase, apart from the quarter-finals and the semi-finals, was played by a single match. 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. In the quarter-finals and the semi-finals were played over two legs, with each team playing one leg at home. 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 away goals were also equal, then extra time was played. The away goals rule was again applied after extra time, i.e. if there were goals scored during extra time and the aggregate score was still level, the visiting team advanced by virtue of more away goals scored. If no goals were scored during extra time, the winners were decided by a penalty shoot-out. In the round of 16, if the score was level at the end of normal time the two-legged rule was applied. The mechanism of the draws for each round is as follows:

First round

The draw took place on 17 August 2006.

Summary

Matches

Second round

The draw took place on 17 August 2006, after the First Round draw.

Summary

Matches

Additional round

Summary

Matches

Bracket

Round of 32

The draw took place on 17 August 2006.

Summary

Matches

Round of 16

The draw took place on 16 November 2006.

Summary

Matches

Replay

Quarter-finals

The draw took place on 11 January 2007.

Summary

Matches

Panathinaikos won 4–3 on aggregate. PAS Giannina won 3–2 on aggregate. Skoda Xanthi won 3–0 on aggregate. AEL won 2–0 on aggregate.

Semi-finals

The draw took place on 11 January 2007, after the quarter-final draw.

Summary

Matches

Panathinaikos won 1–0 on aggregate. AEL won 4–0 on aggregate.

Final

Top scorers