Petrakis began his coaching career in 1991 at Asteras Perama. He took over Ergotelis in 1992, before returning to Asteras Perama in 1994. Up next in 1997, Petrakis was hired by Heraklion-based club Irodotos, whom he promoted to the Gamma Ethniki, the third tier of the Greek football league system. He then took over management of Malia local club PANO Malia, whom he promoted to the Delta Ethnikifor the first time in their history and managed to win the Greek Football Amateur Cup in 2000. He then managed to also promote the amateur department of OFI Crete, OFI 94 to the Delta Ethniki, and was manager from 2000 until 2002, when the club appointed him assistant to OFI's head coachZdeněk Ščasný. In 2003, Petrakis returned to Irodotos, and managed to promote the club to the Gamma Ethniki once again. In 2004, Petrakis left Crete for the first time in his career, taking over management of Arcadian club Asteras Tripoli, whom he also promoted to the Gamma Ethniki. He then returned to Rethymno and led local club Asteras Rethymno to the Gamma Ethniki as well. Petrakis went on to coachNea Ionia, Ionikos and Chania, before returning, and being appointed head coach of OFI on 7 January 2013, where he made his debut as a Superleague manager. Petrakis coached the club in 15 matches, managing to avoid relegation, and terminated his contract with the club at the end of the season on mutual consent. In the summer of 2013, Petrakis was hired as head coach of the other local Superleague side Ergotelis. The season took off with an impressive start, in which the club remained undefeated for 8 consecutive matches. At the end of October however, Ergotelis began struggling, and as a result, the club's board of directors decided to replace Petrakis on 14 January2014.
Fourteen days later, on 28 January 2014, Petrakis was hired by Epirus-based Superleague club PAS Giannina. Petrakis managed avoid relegation at the end of the season, and subsequently went on to secure a 6th-place finish in the 2014–15 and 2015-16, thus leading PAS Giannina to their first ever UEFA Europa League campaign. For this feat, Petrakis was named "Best Manager in Greece" for the 2014–2015 season. Further contributing to the club's history, Petrakis managed to advance PAS Giannina to the Third qualifying round of the competition, after eliminating Norwegian club Odd 4–3 on aggregate.He was candidate for "Best Manager in Greece" for the 2015–2016 season but he didn't voted again.His contract didnt renewed because PAS Giannina relegated from Super League.
