Empoli then played in the two-legged final against Livorno. On 29 May 2013, Hysaj played another full 90-minutes in the first leg of the final against Livorno, finished in the draw 1–1 and another one in the second leg final on 2 June 2013, finished in the loss 1–0, At this way Livorno promoted to 2013–14 Serie A on aggregate 2–1. Hysaj finished 2012–13 season with Empoli, making a total of 35 appearances, by where 30 in league, 1 in Coppa Italia and 4 in Serie B promotion playoffs.