Faraki began his coaching career as an assistant coach at Pas Tehran, the club that he played for in 1976 to 1992. He worked with many coaches like Ebrahim Ghasempour, Firouz Karimi and Bijan Zolfagharnasab. After six years as assistant coach, he was named as caretaker manager of the team after the resignation of Ghasempour in 2002. He led the team until the end of the 1999–00 season which the club ended in 7th place. He left the team after Farhad Kazemi becomes the team's head coach.
During Branko Ivankovic's time as Team Melli manager, Faraki was the assistant manager. He was also the head coach of the Iran national under-23 football team from 2003 till 2006. He was manager of Kaveh Tehran which led the club to promotion to the Azadegan League. He was appointed as head coach of Naft Tehran on 1 July 2010 and secured the team from relegation in his first season at the club. At the second season, he led the club to the 5th place, which was their best league end until 2014. He not renewed his contract with the team and signed a two years contract with Foolad on 5 June 2012. He led Foolad to the AFC Champions League for the second time since 2006 after they finished 4th in 2012–13. In 2013–14 season, Faraki's side won the league, finishing the season with 57 points, two more from runners-up Persepolis. He resigned as Foolad's manager at the end of the season because he needs an imminent knee operation.
On 9 September 2014, Faraki was named as new manager of Sepahan with signing a two-year contract, replaced Zlatko Kranjčar who resigned day before.