Francis started his career Vasco and later moved Salgaocar and Dempo. He was a part of Delhi Dynamos side in the last two seasons.
The Goan winger impressed FC Pune City CEO Gaurav Modwel who said: "Francis has been an asset for all teams he has played for, including the national side.
"His versatility of playing on the wings, attacking midfield or any position that the team needs him in will give the Coach a lot of flexibility.
FC Pune City manager Antonio Habas was delighted to add some experience to the squad. He said: "Francis adds depth to our wing play. He can play as a second line of attack behind our forwards as well as hold the midfield when needed. We hope he continues to be a value add to our team as much as he was to his previous ones."
Fernandes too was excited on joining FC Pune City. He said: "I am thankful to FC Pune City for providing me a new challenge. The club's heart is in the right place and I want to be a part of their glorious time."
FC Pune City Co-owner and Bollywood star Hrithik Roshan welcomed Fernandes and said: "Francis is a wonderful addition to the FC Pune family. His skills will make him an invaluable member of the team. I wish him all the best."