Eguavoen began his coaching career in Malta with Sliema Wanderers, he was given the job as player-coach for the 1999–2000 season, but lasted in that role for only few months.

In the 2008–09 season, Eguavoen was head coach at Enyimba International in Aba, however he left soon after, leading them to a 3rd-place finish in league and winning the Federation Cup.

In June 2010, the Nigeria Football Federation asked Eguavoen to replace Swedish Lars Lagerbäck until he decide his future plans.

[9] On 12 December 2021, Eguavoen was appointed manager of Nigeria on an interim basis for the 2021 Africa Cup of Nations, following the departure of Gernot Rohr.

[10] After Nigeria exited from the round of sixteen with an agonising defeat to Tunisia, he returned to his position as the Technical Director of the side.