In 1984 Obua started a new career as a coach, initially on a part-time basis, with his old club, Police FC. In 1995, he became the full-time coach and, under his guidance, the club gained promotion back to the Super League after a 19-year absence. At the national level, Obua managed the Uganda youth team at the 1991 All-Africa Games and in 1995 he managed the Uganda 'B' team that reached the final of the 1995 CECAFA Cup. In 1998, he was offered the post of coach to the national team, but turned it down. Instead, in December that year, he contested and won the election for president of FUFA. In 2001, he was re-elected to a second term and in 2003 he also became chairman of the Council for East and Central Africa Football Associations (CECAFA).