Čustović started his career at local side Velež Mostar in 1991, before joining Slovenian Second League team Triglav Kranj in 1996.
In 2010, Čustović joined Germinal Beerschot, who loaned him out to the successor of his previous club Mouscron, namely Mouscron-Péruwelz in 2012.
On 2 June 2007, he experienced his first notable moment for the national team by scoring his first international goal when he headed the winner over Turkey from a corner kick taken by Mirko Hrgović.
In September 2017, Yves Vanderhaeghe, Oostende manager at the time, was sacked after a poor start to the season when the club collected only one point in seven games and were bottom of the league.
[6] On 25 January 2020, Čustović was named as an assistant of Bosnia and Herzegovina national team head coach Dušan Bajević.