Born in Vigevano, Lombardy, Varano started his career at Lombard club Atalanta.
[2] On 16 July 2014 Varano graduated from their youth system and joined Serie C club Venezia, along with Simone Magnaghi.
[3] In July 2015, Cesena signed Federico Varano and Moussa Koné from Atalanta for a total transfer fee of €6 million, as part of a cashless swap[4] which Luca Valzania moved to Atalanta from Cesena also for €6M fee on 30 June.
[5][6][7][8][9][10] Cesena also signed Mattia Caldara and Salvatore Molina on temporary basis from Atalanta as part of the deal.
[11] Varano failed to enter the first team lineup in the first half of 2015–16 Serie B season.