On 5 July 2014, Rajaković was named assistant coach of the Oklahoma City Thunder. During his time with the Thunder, Rajaković has helped develop many players, including Steven Adams, Andre Roberson, Terrance Ferguson, Victor Oladipo, Dennis Schröder, and Alex Abrines. Rajaković served as the Thunder’s head coach at NBA Summer League in 2014 and 2015. He was on the Western Conference All-Star Team coaching staff in 2014. Rajaković helped lead the Thunder to the playoffs four consecutive seasons (2016, 2017, 2018, and 2019), making it to the 2016 NBA Western Conference Finals.