During the off-season, Ramírez moved to Atlético Nacional, the club who defeated Santa Fe in the league final just the previous season and the club where Ramírez spent his youth years. Ramírez first season at his new club did not go very well as Atlético Nacional ended eleventh place and missed out of the semifinal stage, three spots lower than his former club Santa Fe who did qualify to the semifinals stage. Injuries in 2006 limited Ramírez to appear in 21 matches in both seasons' tournaments (Apertura and Campeonato Finalización) as Atlético Nacional ended both seasons in the top eight but did not win their respective groups in the semifinals stage. Also in 2006, Ramírez made his Copa Libertadores debut in a 3–2 loss against Palmeiras, Ramírez was substituted by Héctor Hurtado in the 81st minute.