In March 2016, Nishino returned to the Japan Football Association as a technical director. In April 2018, Japan national team manager Vahid Halilhodžić was sacked and Nishino was named as the new manager. In the 2018 World Cup, Japan qualified to the knockout stage, becoming the only Asian team to do so in the World Cup. However, his Japan lost 2–3 to Belgium despite having led 2–0, thus were eliminated from the tournament.