During his professional career, Agayev played in national leagues of Azerbaijan, Turkey, Portugal and Czech Republic.

Agayev began playing football during his school years under his father for local club named Bərəkət.

After his impressive performances for youth team, he joined Shafa Baku and won his first big trophy under Vagif Sadygov in 2001.

He took some unfortunate goals, but did manage to pull off a few impressive exhibitions, securing important results for the team.

[6] He made his Czech First League debut for Mladá Boleslav against Slavia Prague in Eden Arena on 27 August 2017.