Mulee first took charge of Kenya between 2003 and 2004, including at the 2004 African Cup of Nations. Mulee returned for a brief second spell in 2005, which lasted just one day from 16 to 17 December. Mulee returned to Kenya for a third time in March 2007. Mulee's fourth stint in charge of Kenya began in September 2010. Mulee quit the role in December 2010 following a run of three defeats in the 2010 CECAFA Cup. In October 2020, he returned to coach the Kenyan national team for a fifth time.