A Santa Cruz youth graduate, Gilberto made his senior debut on 5 July 2009, coming on as a substitute in a 3–0 Série D away win against CSA. In January 2010, after five first team appearances, he was loaned to Vera Cruz until the end of the year's Campeonato Pernambucano. After scoring twelve goals in 18 appearances, Gilberto returned to Santa and started to feature more regularly. He became an undisputed starter during the 2011 campaign under Zé Teodoro, scoring twelve goals in the 2011 Pernambucano and being chosen as the best striker in the competition.
In May 2011, Gilberto signed a three-year contract with Internacional in the Série A. He made his debut in the category on 28 May, replacing Mario Bolatti in a 1–0 loss at Ceará. Gilberto scored his first goal in the main category of Brazilian football on 16 November 2011, netting the game's only in a home defeat of Bahia. On 7 July of the following year, after being sparingly used, he was loaned to Sport Recife until May 2013. After appearing regularly, Gilberto returned to Inter in January 2013. In July, however, he moved to Portuguesa also in a temporary deal; an immediate starter, he finished the season 14 goals for the club.
On 13 December 2013, Gilberto joined Major League Soccer side Toronto FC for a reported transfer fee of over $3 million, choosing MLS after turning down more lucrative offers from Mexico and Germany. He made his debut with Toronto FC against D.C. United on 22 March 2014, the game ended in a 1–0 home victory. Entering as a substitute against the Columbus Crew on 31 May 2014, Gilberto recorded an assist on Jermain Defoe's 81st-minute equalizer in an eventual 3–2 win to help his team win the Trillium Cup. On 27 June 2014, Gilberto scored his first goal for Toronto FC against the New York Red Bulls, lashing in a 72nd minute free-kick, after arguing with Defoe as to who would take the kick.
Due to the arrival of Jozy Altidore, and Sebastian Giovinco in January 2015, both of whom would take up DP slots, after only one season with Toronto, Gilberto was loaned to Brazilian club Vasco da Gama on 20 February 2015. He was the club's top goalscorer during the 2015 Campeonato Carioca with nine goals, but was demoted to a backup option after the arrival of new manager Celso Roth.
Vasco de Gama terminated the loan in July 2015, forcing Toronto to release Gilberto. He was claimed off waivers and acquired as a designated player by Chicago Fire on 27 July 2015. After scoring five goals in his first season – which included a brace against former club Toronto – Gilberto failed to find the net in his second, and his contract with Chicago Fire was mutually terminated on 29 June 2016.
