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The 37 year-old stated his intention to return to Brazil in April before completing his ninth campaign at the Etihad Stadium, and leaves at the end of his contract having made a total of 383 appearances for City.
Fernandinho took over as City captain after David Silva's 2020 departure and featured in five Premier League title wins, the last four of them under Pep Guardiola's management.
But the holding midfielder, who has won 53 caps for Brazil, was reduced to a supporting role during the 2021-2022 season, starting just 17 games in all competitions as Rodri enjoyed a terrific campaign at the base of Guardiola's midfield.
On Monday, Athletico Paranaense tweeted an image of Fernandinho with club president Mario Celso Petraglia, alongside the caption: "Welcome back, Fernandinho!"
Fernandinho spent three seasons with the Curitiba-based club before joining Shakhtar Donetsk in 2005, where he won six Ukrainian top-flight titles.
Athletico Paranaense are coached by former World Cup-winning Brazil boss Luis Felipe Scolari, who joined the side in May.