Born in Ajuricaba, Brazil, Carlos Eduardo lived in the city until moving to Porto Alegre at age fourteen to join Grêmio's youth system, where he began his career and meet his future teammate, Lucas Leiva.

Grêmio was a very beautiful story, I managed to win there and the club gave me the experience to come here to be able to show my football naturally.

[11][12] In the Copa Libertadores Finals, Carlos Eduardo played in both legs, when his team Grêmio lost to Boca Juniors 5–0 on aggregate.

[15][16] Having established himself in the starting eleven for the side, Carlos Eduardo made thirty–six appearances and scoring seven times in all competitions.

[19] On 29 August 2007, Carlos Eduardo moved for a transfer fee of 8 million euro to 1899 Hoffenheim on a five-year deal and was joined up by Demba Ba.

[23] However, during a match against Paderborn on 21 September 2007, he suffered an abdominal muscle strain that saw him substituted at half time, as 1899 Hoffenheim won 2–0.

[26] Despite being sidelined on two more occasions halfway through the first half of the season, he continued to be a regular player in the first team, playing in the midfield position.

[49] However, in a match against Bochum on 11 April 2009, Carlos Eduardo was given a red card after elbowing Philipp Bönig in a 3–0 loss.

[53] Despite being on the sidelines on three occasions, due to injury and suspension, Carlos Eduardo continued to be a first team regular, as the club finished at seventh place in the league.

Ahead of the 2009–10 season, Carlos Eduardo was linked with a move with Russian side Zenit Saint Petersburg after the club made 15 million bid for him in the summer transfer window.

[71][72] Weeks before leaving the club, he made his last appearance for Hoffenheim in the DFB-Pokal in a 4–0 win over Hansa Rostock amid of the transfer speculation.

[73] On 24 August 2010, Carlos Eduardo was transferred to the Russian Premier League champions Rubin Kazan for a fee of 20 million euro over 18 months and signed a four-year contract.

[75] On 11 September 2010, Carlos Eduardo made his Rubin Kazan debut and scored twice in a 3–0 win over Amkar Perm.

[77] Three days later, on 14 September 2010, Carlos Eduardo made his UEFA Champions League debut, starting a match and played 77 minutes before being substituted, in a 1–0 loss against Copenhagen.

It was reported from Sports Express on 30 September 2011 that Carlos Eduardo made his return to training after being sidelined for almost ten months.

[90] After his return, Carlos Eduardo struggled to fight for his place in the first team, due to loss of form, as well as, his own injury concern.

[95] As a result, Carlos Eduardo apologised to Volga supporters for his action and Sapogov ended up banned for three matches.

[123][124][125] It wasn't until on 27 August 2015 when he scored the only goal of the game against FK Rabotnički to help the side qualify for the UEFA Europa League Group Stage.

On 25 January 2013, Carlos Eduardo returned to Brazil after a five-year absence by joining Flamengo on loan and stayed for one and a half year, until 30 June 2014, while also extending his contract with Rubin Kazan until the summer of 2016.

[136] Carlos Eduardo made his Flamengo debut on 6 April 2013, in a 1–1 draw against Duque de Caxias, but suffered a muscle injury in the process.

[138] After recovering from injury, he made his league debut in the opening game of the season, coming on as a substitute in the 75th minute, in a 0–0 draw against Santos.

[139] However, Carlos Eduardo struggled to regain his first team place, he was mainly put on the substitute bench and made twenty–four appearances for Flamengo.

[148] On 14 May 2016, Carlos Eduardo made his Atlético Mineiro debut, in the opening game of the season, where he played 56 minutes before being substituted, in a 1–0 win over Santos.

[159] After leaving Atlético Mineiro, it was announced on 27 June 2017 that Vitória signed Carlos Eduardo until the end of the 2017 season.

[161][162] Carlos Eduardo made his Esporte Clube Vitória debut, starting a match and played 57 minutes before being substituted, in a 0–0 draw against Bahia on 2 July 2017.

[164][165][166][167] However, Carlos Eduardo found his first team opportunities limited, due to being on the substitute bench for the rest of the season.

[177] Carlos Eduardo made his Coritiba debut, coming on as a 62nd-minute substitute, in a 1–0 loss against Atlético Clube Goianiense on 18 August 2018.

[178] However, during a 2–0 loss against Oeste Futebol Clube on 24 August 2018, he suffered a muscle injury in the 13th minute, resulting in his substitution and was sidelined for two months.

[179] It wasn't until on 17 October 2018 when Carlos Eduardo returned to the first team, coming on as an 82nd-minute substitute, in a 1–1 draw against Centro Sportivo Alagoano.

[188] After the injuries of Luís Fabiano and Elano, Carlos Eduardo and Grafite were brought into the squad against Republic of Ireland, appearing as an 84th-minute substitute, winning 1–0 on 2 March 2010.