At age 18, Siqueira was signed by Internazionale from Ipatinga in August 2004, at first in temporary deal for €125,000. He also played for hometown clubs Figueirense and Avaí before joining Inter. In January 2006, as part of César's transfer, he went on loan to Lazio, which included an option to co-own the players rights at the end of season.
Udinese
On 11 August 2006, Siqueira joined Udinese in a co-ownership deal, for €750,000. Siqueira never became a regular for Udinese and made 3 starts and 13 substitute appearances in the 2006–07 season. He made his Serie A debut on 10 September 2006 in a 1–0 loss to Messina. During the 2007–08 season, Siqueira remained at Udinese but was seldom used. As Udinese did not buy full ownership from Inter, the out-of-favour Siqueira was loaned to Ancona to join another Inter-owned player, Rincón. During the 2008–09 season with Ancona, Siqueira featured regularly for the newly promoted club making 24 league appearances and scoring his first professional goal. In June 2009, he returned to Udinese as the club now had Siqueira's entire registration rights. On 10 January 2010, he substituted Paolo Sammarco in the 71st minute, his first match of the season. He then made two more substitute appearances for the club.
Granada
In 2010, Siqueira joined Granada on loan as part of a partnership agreement with Udinese in which various players joined Granada from the Italian club. In his first season in Spain, Siqueira featured regularly for his new club and helped Granada gain promotion to La Liga, despite being sent off 3 times in 34 league matches. After a fine first season with Granada, on 30 June 2011 he penned a four-year contract to remain with the club, as his contract with Udinese expired. On 20 March 2012, Siqueira scored an audacious meisteresque dink from the penalty spot against Barcelona in La Liga at the Camp Nou. Siqueria soon started to attract from other clubs to sign him. At one point, Valencia and Benfica were keen to sign him. However, Siqueira signed a further contract extension, which will keep him until 2017. At the end of the 2012–13 season, which left the club in 15th position, Siqueira announced he intended to leave the club in the summer transfer window. Siqueira, however, denied he wanted to leave the club and said he was happy there in an exclusive interview with Marca. Despite this, Siqueria retained interest from English Premier League sides Everton, Liverpool and Stoke City. In April 2014, Real Madrid made a bid for Siqueria from Granada and the move was agreed. However, this was denied by the club's president, Enrique Pina.
Benfica (loan)
On the very last minutes of the summer transfer deadline day, Siqueira signed a season-long loan deal with Benfica, with an option to make the move permanent for €7 million. He played in the club's 2-0 victory over Rio Ave in the 2014 Taça da Liga Final, and 99 minutes of the loss to Sevilla on penalties in the 2014 UEFA Europa League Final. Benfica also won the Primeira Liga title, with Siqueira playing 18 matches and scoring once, in a 2-0 win over Nacional on 27 October.
Atlético Madrid
On 6 June 2014, Atlético Madrid and Granada reached an agreement for the transfer of Siqueira for a reported €10 million fee, pending a medical examination. He signed a four-year contract after passing his medical, on 11 June2014. Upon joining the club, Siqueira said that "it did not take a second to decide" to join Atlético. Siqueira made his debut in a friendly match against Numancia, on 23 July 2014, which Atlético won 1–0. He made his competitive debut in the first leg of the 2014 Supercopa de España on 19 August, a 1-1 draw away to Real Madrid in which he played 64 minutes before being replaced by fellow debutant Cristian Ansaldi.
Valencia (loan)
On 1 February 2016, Siqueira was loaned to Valencia.
Retirement
Having been without a club for over a year, he announced his retirement on 29 August 2018.
