Sepahan was eliminated from Champions League with a 4–1 defeat to Al-Ahli. After this, Alireza Marzban, the assistant of Kranjčar in Sepahan parts away his contract with Sepahan and left his job. Sepahan changed a win with draw in match with Saba Qom with a 90+4 goal. Sepahan suffered the heaviest defeat in league under Kranjčar (and also second in history of Iran Pro League) in match against Tractor Sazi 4–1 and defeated Naft Tehran 4–3 which was 1–3 until the twenty minutes remaining. Sepahan suffered the third home lost in match against Esteghlal with a goal from former Sepahan player, Khosro Heydari. Sepahan defeated newly promoted Gahar Zagros 2–1 with a late goal from Mohammad-Reza Khalatbari and Damash Gilan 3–0. At the final match of the first half of the league, Sepahan made a 1–1 draw with Aluminium but earn the title of winter champions after Esteghlal lost to Damash. Zlatko Kranjčar's side was faced with Foolad in Round of 32 of Hazfi Cup on 13 December 2012 which defeated them 2–1 at Isfahan. They defeated Mes Rafsanjan, Sanat Naft and Esteghlal on next matches to reach to the final. In final, his side won against Persepolis 4–2 on penalties to crown their 4th domestic cup title in last ten years. In his second season as Sepahan head coach, his side finished in third place, three points behind winner, Esteghlal. Kranjčar renewed his contract with Sepahan on 14 May 2013 for two more seasons despite offers from Persepolis, Tractor Sazi, Rapid Wien, Al-Hilal and Al-Wasl. Yaghoub Karimi, Ali Hamoudi, Shoja' Khalilzadeh and Mojtaba Jabbari joins the team, Hadi Aghili and Rahman Ahmadi also returns to the team and Arash Afshin joined on loan from Foolad in the summer transfer window. Ahmad Jamshidian also left the team to Esteghlal, Mohammad Bagher Sadeghi sold to Saipa and Milan Susak, Mohammad Reza Khalatbari and Farshid Talebi were transferred to Al-Wasl, Ajman and Tractor Sazi.