Faraki replaced Croatian coach Zlatko Kranjcar in September 2014 and led the Isfahan-based team to win Iran Professional League (IPL) title.
Sepahan lost to Esteghlal 3-0 last week and was held to a 1-1 draw by struggling Esteghlal Ahvaz on Saturday.
“Things just don't seem to be working out for me and I decided to quit my job in the team," Faraki said.
"I have nothing more to say because I think Sepahan needs concentration at the moment since they will play in Iran’s Hazfi Cup on Thursday,” Faraki said.