Juninho Pernambucano joined Vasco da Gama in 1995. He won several trophies during his first stint with the club, including the Brazilian Championship in 1997 and 2000, the Copa Libertadores in 1998, the Copa Mercosur in 2000, as well as the 2000 Brazilian Silver Ball award as one of the best Brazilian midfielders of the season. At that time, he was playing with Romário, Edmundo, and Juninho Paulista, and he became a favourite of the Vasco fans. Since that time he has been known as Reizinho de São Januário (The Little King of São Januário), a reference to Vasco da Gama’s stadium, as well as Reizinho da Colina (The Little King of the Hill).

On 7 September 1999, Juninho Pernambucano played two top-level matches in two different countries in the same day. He represented his country in the second half of the friendly match between Brazil and Argentina in Porto Alegre, which Brazil won 4–2, playing about fifteen minutes. In spite of a delayed flight to Montevideo, he managed to arrive in Uruguay in time to feature in the second half of the Copa Mercosur match between Vasco and Nacional. He took part at the 2001 Copa América with Brazil.

In 2001, the player won a preliminary injunction against Vasco da Gama, after which he became a free agent. Although he left Vasco for Lyon after a judicial fight, he is still considered a favourite of Vasco fans. Juninho has been cited in a classic chorus sung by the fans remembering his free-kick goal against River Plate at River Plate Stadium, during the 1998 Libertadores which helped the club reach the finals against Barcelona de Guayaquil. Juninho played 295 games for Vasco from 1995–2001.

In 2001, Juninho moved abroad to play for French club Olympique Lyonnais. Before his arrival at Lyon, the club had never won the French championship. Starting out in his first season at the club, Olympique Lyonnais won seven league titles in a row; along with his former Lyon teammates Grégory Coupet and Sidney Govou, he holds the record for most Ligue 1 titles won (seven), along with Hervé Revelli and Jean-Michel Larqué of Saint-Étienne, as well as Thiago Silva and Marco Verratti of Paris Saint–Germain. At Lyon, Juninho made himself especially noted for his accurate, powerful and varied set pieces. As well as often being ranked the world’s greatest free kick exponent, Juninho was a noted passer, providing many assists, and his leadership abilities prompted Lyon manager Gérard Houllier to name him team captain.

Although Juninho had a period of prolonged domestic success during the 2000s, that contributed to him being considered as one of the best Brazilian players in the world at the time, he was not selected for the Brazilian squad that featured in the 2002 FIFA World Cup and in the 2004 Copa América missing both because of a recurring knee injury. Brazil would win both tournaments. He was however a member of the Brazil squad that won the 2005 FIFA Confederations Cup.

In the 2006 FIFA World Cup Juninho scored against Japan in a group stage match. Following Brazil’s defeat to eventual runners-up France in the quarter-finals of the tournament, he announced his international retirement, so as to make way for younger talents coming through the ranks in Brazil, in order to build for the 2010 FIFA World Cup.

Juninho has scored from free-kicks beyond 40 yards on a number of occasions: including against AC Ajaccio in 2006, against Barcelona in 2007, against OGC Nice in 2008, and a strike against Marseille in 2009, this being his final free kick goal for Lyon. Even before Lyon, he displayed his talent at Vasco da Gama, scoring several free kick goals for the club. Juninho has also scored memorable free kick goals for Brazil, the most famous being a curling shot from 30 yards against Greece in the 2005 FIFA Confederations Cup. Brazil would go on to win the match 3–0. Also, Juninho scored two free kicks against Nice in the 2008–09 season as Lyon were losing 2–0, with his second from 48 yards out. Juninho’s free-kick style has been adapted by several other players, such as Andrea Pirlo, Cristiano Ronaldo, Didier Drogba, and Gareth Bale. The knuckle ball free-kick technique takes a significant amount of skill to replicate and strike accurately. In total, Juninho scored 75 official goals from direct free kicks throughout his professional football career, which spanned from 1993 to 2013.

Juninho Pernambucano scored 100 goals while at Lyon. Forty-four of those goals were scored from free-kicks, the last of which was a strike from long distance against Olympique de Marseille. He scored his 100th goal on his very last game for Lyon, through a penalty kick against Caen. Juninho was also a prolific goalscorer in the Champions League, and he matched Sonny Anderson as the club’s top goalscorer in European competitions with 16 goals, on a match against Steaua Bucharest in November 2008. He later became Lyon’s top goalscorer in the Champions League with 18 goals, while reaching three quarter-finals in the competition.

On 26 May 2009, Lyon chairman Jean-Michel Aulas announced in a press conference that the club had accepted Juninho’s request to leave Lyon at the end of the season as a free agent, despite the fact that the player still had a year left in his contract. During the press conference, Juninho sat next to Aulas and left without saying a word.

On 17 June 2009, Juninho signed a €2.5 million, two-year contract with Qatari club Al-Gharafa. In his first season with the club, Juninho captained the team to their seventh league title and wins in the Qatari Stars Cup and Qatar Crown Prince Cup, completing the treble. He finished the season with Player of the Year honours from the Qatar Football Association. Juninho played 66 games for Al-Gharafa Sports Club and scored 25 goals.

On 27 April 2011, Juninho rejoined his former club Vasco da Gama. He scored his first goal for them in his first game back, via a freekick against Corinthians. He scored another 2 free kicks and a penalty during the course of the Brazilian top flight season. On 28 March 2012, he played and scored a goal for a 4–1 lead in Edmundo’s farewell game against Barcelona Sporting Club. Vasco went on to win this game 9-1. Juninho then scored a trademark free kick against Esporte Clube Bahia in the fourth round of the Campeonato Brasileiro; that goal was to be his 16th since returning to Vasco from Al-Gharafa Sports Club.

In July 2012, Juninho extended his contract with Vasco for 6 months. On 18 July 2012, he made his 350th appearance for the club against São Paulo FC. In August 2012 he played against his youth team Sport Club do Recife and scored a free kick goal, which was his fourth goal from free kicks in Campeonato Brasileiro Série A 2012. Juninho played in 370 official matches for Vasco scoring 88 goals.

On 17 December 2012, Juninho signed for Major League Soccer team New York Red Bulls. He made his first appearance for the team on a friendly match against Malmö, in which he was a starter. On 3 March 2013 Juninho made his official debut for Red Bulls, playing the full time in a 3-3 draw against Portland Timbers. On 3 July 2013 NY Red Bulls announced that they reached an agreement with Juninho for the cancelation of his contract. The midfielder featured in 13 games for the New York Red Bulls, providing the team with four assists.

On 11 July 2013, Vasco da Gama announced Juninho’s return to the club. The player scored and assisted in his third debut for Vasco, in a 3–1 victory against rivals Fluminense. He scored his first home goal of the season against Criciúma with a 32-metre free kick, also assisting Edmílson for the third goal of the game. He played his third game for Vasco da Gama against another rival team Botafogo, setting up Andre for Vasco’s first goal, in a 3–2 defeat. He played his sixth game against Grêmio and made another assist. It was his fourth assist in Campeonato Brasileiro. Juninho made his fifth assist against Sport Club Corinthians Paulista; the game ended in a 1–1 draw. He played his 16th game against Vasco rivals Botafogo and made two assists; the game ended with a 2–2 draw after Botafogo had led 2–0. Juninho played 16 games for Vasco in his third stint with the club, scoring 2 goals and making 7 assists in the Campeonato Brasileiro.

He retired from playing professional football on 2 February 2014. During his years at Vasco da Gama, Juninho won six titles: the Brazilian Championship in 1997 and 2000, the Campeonato Carioca in 1998, the Rio-São Paulo Tournament in 1999, the Copa Libertadores in 1998, and the Copa Mercosur in 2000.

Following his retirement, Juninho worked as a football commentator for Brazilian sports network Rede Globo, a stint that ended up in 2018.

In May 2019, Juninho was appointed as the director of football of his former club Olympique Lyonnais. His first decision was to name former Brazilian international teammate Sylvinho as the head coach of the French Ligue 1 team.

Juninho is one of the few footballers to publicly speak out against racism in the country, as well as criticize Jair Bolsonaro, the far-right president of Brazil that assumed office on 1 January 2019. He is a father and a grandfather.