Molina started his career in Colombian side Envigado at the age of 16. He soon made his way up to the first team and was transferred to Independiente Santa Fé. around his stint through Santa Fe, After a serious injury he returned to the pitch in 2002 playing for Independiente Medellín where he led the team to its first national championship in 45 years and the third overall. In 2003 he helped the team reach the semi-finals of the Copa Libertadores. After the successful campaign with Independiente Medellín he moved to CA Morelia of Mexico until 2004. After Morelia, Molina went to the United Arab Emirates (UAE) to play for the Al Ain FC where he stayed for a semester, after which he returned to his best memories with Independiente Medellin for another semester. Molina then played for San Lorenzo de Almagro of Argentina from 2005 to 2006. In 2007, Molina signed with ParaguayanClub Olimpia de Asunción where he played the first semester of the year. After a very successful campaign with the team in which he was the co-scorer with 10 goals, Molina was transfer for the second semester of 2007 to the Serbian club FK Crvena Zvezda, also known as Red Star Belgrade, in which Molina makes his debut in the European football.
In July 2009, Molina moves to South Korean club Seongnam Ilhwa Chunma for $1,275,000. In his first K-League match for Seongnam, he scored debut goal against Pohang Steelers. In all K-league competitions Molina scored 22 goals along with 11 assists in 50 appearances for Seongnam Ilhwa Chunma and in 2010 Molina and Seongnam Ilhwa Chunma won the AFC Champions League 2010.