When he was 15 years old, he traveled from Cartagena and joined
Deportivo Cali's youth ranks, before making his debut with
Atlético Nacional in the 2002 Finalizacion. In the 2005 Apertura he won his first title as a professional after Nacional beat
Independiente Santa Fe in the finals. In 2006, he joined Santa Fe. Marrugo joined
Deportes Tolima in 2008. He was part of the squad that finished runner-up to
Once Caldas in 2010 Finalizacion. On 27 February 2011, he provided two assists in a 3–2 away victory to Cucuta. On 3 April 2011, he scored once and had three assists in a 7–4 victory away to
Atlético Huila. On 7 May 2011, he scored in a historic 5–0 home victory against his former club Atletico Nacional. On 26 May 2011, he scored in a 3–1 victory against
Cúcuta Deportivo in the playoffs quarter-finals. On 28 October 2012, Marrugo scored twice in five minutes to give Tolima the three points in a victory against
Deportes Quindío. In November 2012, after more than 200 games for Tolima, he has his first experience outside Colombia and joined Mexico's
Pachuca. The following year, he was loaned out to
Veracruz. In the beginning of 2014,
Deportivo Cali acquired Marrugo to enforce the midfield for the
Copa Libertadores and 2014 Apertura. For the second semester of 2014, he was signed by
Independiente Medellín. In the first matchday, he scored the only goal of the match in El Clasico Paisa. In his first season, he scored 3 goals and provided 11 assists in 22 appearances, helping the club finish runner-up to Santa Fe; the same occurred in the 2015 Apertura, this time against Deportivo Cali. In 2016, he helped Independiente Medellín win their sixth league championship, scoring a brace in the final against
Junior. In the 2016 Clausura, he scored 7 goals. 2 of those came against Boyaca Chico on 6 November 2016; with Medellin losing 2–1 at the 80th minute, Marrugo scored twice to give
El Poderoso the 3–2 lead. On 28 May 2017, he scored in a 4-3
clásico paisa victory. On 21 July 2017, Marrugo joined Mexico's
Puebla. In June 2018 he joined Millonarios. On 14 April 2019, Marrugo scored twice and provided an assist in a 3–1 away victory against
Patriotas Boyaca. In 2020 he joined Rionegro Aguilas. In the 2021 Finalizacion he scored 4 goals and provided 9 assists. In 2024 he joined Real Cartagena of the
Categoría Primera B. ==International career==