On 7 March 2015, it was reported that Halilhodžić would take over as the Japan national team's new manager. He was officially appointed on 12 March, replacing Javier Aguirre, who had been sacked over his involvement in a 2011 match-fixing investigation in Spain. Prior to this appointment, Halilhodžić was one of the shortlisted candidates for managing Bosnia and Herzegovina, but he rejected that offer after having two meetings with the Bosnian Football Association. In June 2016, Halilhodžić's Japan hosted Bosnia and Herzegovina in the 2016 Kirin Cup, losing 1–2.