In 2009, Daei turned down a job offer as manager of Rah Ahan.
It was widely believed that Daei could be next in-line for the coaching position of Persepolis but the club chose Zlatko Kranjčar.
On 28 December 2009 Daei was chosen as coach of Persepolis.
At the end of the 2009–10 Season, Persepolis finished fourth in the league but they became Hazfi Cup champions.
In the Hazfi Cup final, Persepolis defeated Azadegan League side Gostaresh Foolad Tabriz 4–1 on aggregate to qualify for the 2011 AFC Champions League.
In the 2010–11 season, Persepolis finished fourth in the league and was eliminated in the group stage of the 2011 AFC Champions League but at the end of the season Persepolis won the 2010–11 Hazfi Cup after defeating rivals Sepahan, Foolad and Malavan.
Daei had many people against him while at Persepolis including the chairman Habib Kashani and after a contention with Kashani, he stated that "I won't work with Kashani Anymore".
On 20 June 2011, Technical committee of Perspolis re-appointed Daei as Persepolis's head coach but he resigned on 21 June.
The technical committee chose Hamid Estili as Daei's successor on that day.
During his time at Persepolis, Daei brought up many youngsters such as Hamidreza Ali Asgari and Saman Aghazamani and other players such as Hadi Norouzi and Maziar Zare were chosen for Team Melli thanks to Daei.
Despite the fact that many challenges and difficulties such as the leaders of fans and the clubs' Chairman Kashani were in Daei's way, Persepolis was crowned Hazfi Cup Champions for two successive years and the fans themselves always loved and cheered Daei but at the same time they did not cheer for any player.
Under the management of Daei, Persepolis won back to back trophies for the first time in 13 seasons.
In 2009, Daei turned down a job offer as manager of Rah Ahan. It was widely believed that Daei could be next in-line for the coaching position of Persepolis but the club chose Zlatko Kranjčar. On 28 December 2009 Daei was chosen as coach of Persepolis. At the end of the 2009–10 Season, Persepolis finished fourth in the league but they became Hazfi Cup champions. In the Hazfi Cup final, Persepolis defeated Azadegan League side Gostaresh Foolad Tabriz 4–1 on aggregate to qualify for the 2011 AFC Champions League. In the 2010–11 season, Persepolis finished fourth in the league and was eliminated in the group stage of the 2011 AFC Champions League but at the end of the season Persepolis won the 2010–11 Hazfi Cup after defeating rivals Sepahan, Foolad and Malavan. Daei had many people against him while at Persepolis including the chairman Habib Kashani and after a contention with Kashani, he stated that "I won't work with Kashani Anymore". On 20 June 2011, Technical committee of Perspolis re-appointed Daei as Persepolis's head coach but he resigned on 21 June. The technical committee chose Hamid Estili as Daei's successor on that day. During his time at Persepolis, Daei brought up many youngsters such as Hamidreza Ali Asgari and Saman Aghazamani and other players such as Hadi Norouzi and Maziar Zare were chosen for Team Melli thanks to Daei. Despite the fact that many challenges and difficulties such as the leaders of fans and the clubs' Chairman Kashani were in Daei's way, Persepolis was crowned Hazfi Cup Champions for two successive years and the fans themselves always loved and cheered Daei but at the same time they did not cheer for any player. Under the management of Daei, Persepolis won back to back trophies for the first time in 13 seasons.
Ali Daei