The 53-year-old resigned as managing director of football in April 2023 after an appeal against a ban over his role in transfer deals and finances while at former club Juventus was rejected by Italy's top sports body.
He and Juventus both denied wrongdoing, and he returned as a Sporting Director in October to work alongside Johan Lange after serving a ban.
"We have agreed that Fabio will return to Italy following the conclusion of the January transfer window, in line with his wish to move back home," Tottenham Hotspur Chief Executive Officer Vinai Venkatesham said in a statement.
"Our management structure is designed to be resilient to personnel changes, and it will be business as usual moving forward."
Paratici will return to try to help Fiorentina away from the Serie A relegation places.
"I want to thank Vinai and the Board of Tottenham Hotspur for accommodating my desire to return to Italy and join Fiorentina," he said. "I have loved my time at the club, however, this opportunity, together with the need to be based in my homeland, has led me to this decision."