Born in Diadema, Gérson Magrão started his career with Cruzeiro in 2004 but didn't make a league appearance before leaving to join Dutch Eredivisie club Feyenoord, he remained with the Rotterdam club until 2007 when he left to return to Brazil after appearing in just six league matches. On his return to Brazil, Gérson Magrão had a short stint with Flamengo before signing with Ipatinga for two years. He played 26 times for Ipatinga and scored his first professional league goal in a 4–2 defeat away to Atlético Mineiro on 13 June 2008. After his spell with Atlético Mineiro, he return to his first professional club Cruzeiro where he made 28 appearances between 2008 and 2009, he scored twice for the club during that time. He made his Copa Libertadores debut with Cruzeiro on 19 March 2009 against Club Universitario. In 2009, Gérson Magrão left Brazil for the second time in his career as he agreed to join Ukrainian side Dynamo Kyiv, who were the defending Premier League champions at the time. He made his Dynamo debut on 23 August against Vorskla Poltava, three weeks later he received his first career red card in a Ukrainian Cup match versus Metalist Kharkiv. Things improved for Gérson Magrão later that month as he played and scored on his UEFA Champions League debut on 16 September against Rubin Kazan, he played in all six of Dynamo's 2009–10 group stage fixtures as the club finished bottom of a group that also included Barcelona and Inter Milan. He made a total of 28 appearances in his debut season with Dynamo. He made just 10 appearances for Dynamo in their 2010–11 season before departing the club at the beginning of the 2011–12 season. Gérson Magrão spent the 2012 season with Santos, before playing with Figueirense for the 2013 season. He signed for Portuguese club Sporting CP in July 2013. Magrão left Sporting in May 2014, after only one season with the club after making just ten appearances in all competitions; during his time in Portugal he played five times and scored one for Sporting CP B. On 30 April 2015, Gérson Magrão joined Série B side CRB. He made 19 appearances and scored twice for CRB during 2015 in Série B, whilst also making one appearance in the Copa do Brasil. In 2016, Gérson Magrão signed for Piracicaba and made his debut for the team on 17 February in the Campeonato Paulista. In total, he made 5 appearances and scored once before leaving on 12 April.
