[4] Zé Roberto started in the youth ranks of Palestra de São Bernardo but it was while playing for Portuguesa, as a left-back, that he became known throughout Brazil after finishing as runner-up in 1996 Campeonato Brasileiro Série A.

[5] He was also part of the Madrid's 1997–98 UEFA Champions League winning squad,[6] scoring his only goal for the club in the opening group match against Rosenborg BK,[7] before moving back to Brazil to play for Flamengo midway through the season.

In an interview in 2012, Zé Roberto spoke of his decision to leave Madrid because of his ambition to play for Brazil at the 1998 FIFA World Cup in France and had limited opportunities to prove his talents in Spain.

On 4 December 2001, he opened the scoring with a curling free kick against Deportivo de La Coruña in the 64th minute, as Bayer comprehensively beat the Spanish side 3–0 in the second group stage of the Champions League.

[11] Following Bayer's victory over Liverpool in the quarter-finals of the Champions League on 9 April 2002,[12] Zé Roberto announced that he would be joining former teammate Michael Ballack at Bayern Munich.

[13] Despite the transfer distractions, Zé Roberto helped Bayer reach the final of the Champions League on 15 May 2002, losing 2–1 to former club Real Madrid in Glasgow.

In May 2002, Zé Roberto joined Bayern Munich for a reported fee of €12 million, signing a three-year deal, linking up with emerging German talent Sebastian Deisler and former Leverkusen teammate Michael Ballack.

Following the announcement that he would not return to Bayern Munich, he publicly criticized the club's style of play and predicted struggles if changes were not made.

In June 2007, it was announced that Zé Roberto would return to Bayern Munich, which paid one million euro to Nacional for a two-year loan.

The revitalised Zé Roberto demonstrated all his newly acquired skills by scoring five goals and forming a rock-solid partnership with Mark van Bommel in his new role in central defensive midfield.

[28] After a season with Qatari outfit Al-Gharafa, Zé Roberto returned to Brazil in May to join Grêmio FBPA in Puerto Alegre, helping them finish third in the Campeonato Brasileiro Série A.

[31] He was immediately appointed team captain, helping them win the 2015 Copa do Brasil with four goals scored in the competition and a successful penalty in the final.

[38][46] He started his career as an attacking full-back or wing-back on the left flank, occasionally functioning in a box-to-box role in midfield; he was later deployed as a left-winger and subsequently in a more creative role as an attacking midfielder, although he struggled to find space in the national side in this position due to the presence of several other world-class playmakers in the squad.

[38] During his time at Bayern Munich, Zé Roberto excelled alongside van Bommel as a defensive midfielder due to his ability to read the game, break down opposing plays and subsequently start counter-attacks; his adeptness at this new holding role led him to be called up to the Brazil national team once again, where he also formed an effective and consistent defensive midfield partnership with Emerson.

"[50] He defended Brazil manager Tite's decision to call up Dani Alves to play in the 2022 FIFA World Cup.