Early in his football career, Emmanuel Amuneke won domestic league titles in Nigeria and Egypt, while playing for Julius Berger F.C. and Zamalek SC, respectively.
In 1994, he signed for Sporting Clube de Portugal, scoring seven league goals in his first season, including one against S.L. Benfica in the Lisbon derby (1–0 home win on December 1st, 1994) and adding the campaign's Portuguese Cup. One of his greatest achievements came in 1996 when he scored the winning goal in the final of the football competition at the Olympic Games, which secured Nigeria their olnly Gold medal till date in Olympic football. In that same year, during the December transfer window, Amuneke was bought by La Liga giants FC Barcelona for $3.6 million.
Since his playing days ended, he has gone on to coach in the Nigeria Professional League and also the Nigeria youth national teams, winning the FIFA World Cup
with the U17s in 2015. He is currently manager for Sudanese Premier League club, Al Khartoum Watani.