Sekou Koita started playing football for Union Sportive des Clubs de Kita and Centre Latika de Bamako. He had his first senior appearances for AS Bakaridjan, then he played for USC Kita. In 2017 he came to Austria, signing for the Austrian side FC Red Bull Salzburg. At the moment he is playing for FC Liefering on loane in Austrias 2nd league.