At an early age, Badelj was already spotted as a possible replacement for Luka Modrić, a key figure in the Dinamo Zagreb first-team squad that joined Tottenham Hotspur in 2008.

He made his senior debut for Dinamo in Champions League qualifier against Northern Irish club Linfield.

[7][8] In the 2011–12 season, Badelj was one of the key players in the Dinamo squad that reached the 2011–12 UEFA Champions League group stage for the first time in 12 years.

[10] Badelj joined Hamburger SV of the Bundesliga in August 2012 for an undisclosed fee thought to be in the region of €4.5 million, according to the Croatian media.

[13] On 31 August 2014, it was announced Badelj had signed for Serie A side Fiorentina for a fee believed to be in the region of €5 million.

[14] In 2018, after the sudden death of Davide Astori due to cardiac arrest in early March 2018, Badelj was appointed as team captain.

[17] On February 20, 2021, he scored his first goal for the club, as he equalized at the last minute of a match against Hellas Verona: in that occasion, he celebrated by recreating the number 13 with his fingers pointed to the sky, as a way to pay tribute to his late friend and former team-mate Davide Astori (in fact, the Italian defender had used to wear the number 13 shirt until his tragic death).

[23] He scored his first goal of the tournament in a 2–1 win over Iceland; helping Croatia en route to topping the group on maximum points.