Benfica
On 15 December 1960, Eusébio arrived in Lisbon, when he was 18 years old. However, he only joined Benfica in May 1961, as a 19-year-old, after the transfer from his local club Sporting Lourenço Marques for 400,000 Portuguese escudos (equivalent to €193,219 in 2023) was finally unlocked. It was a lengthy process and the legality of the signing was disputed by Sporting CP, who also tried to sign him. In the first few weeks of 1961, the Portuguese Directorate-General for Sports ruled in favour of Sporting CP's interests; soon after, the Portuguese Football Federation ruled in favour of Benfica's arguments. The agreement to sign Eusébio with Benfica's local representative (Rodrigues de Carvalho, a major) had been mediated in Mozambique, in June 1960, by one of Eusébio's brothers who was an engineer by training and intervened as an informal sports agent on behalf of his brother, and included the payment of 250,000 Portuguese escudos to Elisa Anissabene, Eusébio's mother (an initial offer of 110,000 escudos which raised to the final 250,000 escudos in November amid growing interest from other football clubs). Benfica discovered Eusébio through the efforts of Brazilian former player José Carlos Bauer, who saw him at Lourenço Marques in 1960. Although he preferred playing with his right foot, Eusébio could use his left just as well. At times, Eusébio would surprise opponents with his dribbling ability, seemingly a talent he preferred to keep secret. Bauer first recommended Eusébio to his former club, São Paulo, but they turned him down.
Bauer had been asked by his former coach at São Paulo, Béla Guttmann, to keep an eye out for talented players during a ten-week tour to Africa, and when São Paulo could not afford the asking price for Eusébio, Bauer then recommended him to Guttmann, who was coaching Benfica at the time. Guttman moved quickly and signed him.
Sporting Lourenço Marques was an affiliate team of Sporting CP, and the Portuguese club disputed the legality of his transfer to Benfica. Eusébio once said: "I used to play for Sporting's feeder club in Mozambique. Benfica wanted to pay me in a contract to go [to Portugal] while Sporting wanted to take me as a junior player for the experience with no monetary reward. Benfica made a nice approach. They went to speak to my mum, my brother, and offered €1,000 for three years. My brother asked for double and they paid it. They signed the contract with my mother and she got the money. [...] Sporting tried to spread the story that I'd stitched them up, but it was the other way round, because they tried to take me for free while Benfica were willing to pay."
Hilário, a friend of Eusébio since childhood and former colleague at the Mozambican club, tried to convince Eusébio to go to Sporting CP. Hilário went to Benfica's dorms, met Eusébio there and Eusébio left the building with Hilário. On behalf of Sporting CP, Hilário offered him an improved professional contract instead of a trial period at the club. Sporting CP's contract offer was double Benfica's, included the necessary funds to allow financial compensation to Benfica for the incurred costs to date, and, according to Hilário, he was successful in that endeavor, but at the end of the day he left Eusébio to rest overnight back in the dorms. Benfica found this meeting suspicious and instructed Eusébio to be codenamed Ruth Malosso. Moreover, fearing a "kidnapping" attempt by Sporting CP, Benfica moved Eusébio on 8 April 1961 to a holiday home owned by Domingos Claudino, former president of Benfica, and a hotel near the Meia Praia beach, in Lagos, Algarve region, where he would remain for twelve days until the transfer upheaval calmed down (Eusébio was awarded his 4th grade diploma while he was hidden in the Algarve). Fearing that Eusébio would "escape", Benfica's representatives reportedly warned him of the "danger of being run over". Eusébio then told his mother: "Mum, I'm going back because there are men here who want to hurt me." In the early hours of 13 May 1961, those in charge of Eusébio's transfer to Benfica occasionally bumped into Jaime Catarino Duarte, son of António Catarino Duarte who was the president of the club at the time, and the son of the president wanted to know where the case stood. He was told that almost everything had been taken care of, with just 400,000 escudos (400 contos) missing before Eusébio could finally be registered by Benfica. Catarino Duarte provided the necessary funds and the transfer was finalized.
The transferring of Eusébio's registration from Sporting Lourenço Marques to Benfica was concluded and he made his first appearance for them against Atlético Clube de Portugal in a friendly game on 23 May 1961. He scored a hat-trick in a 4–2 victory. His debut in an official match was on 1 June 1961, against Vitória de Setúbal, in the third round second leg of the 1960–61 Taça de Portugal. The game was controversially scheduled for the day after the European Cup final against Barcelona and the Portuguese Football Federation did not postpone it. As the first team was returning from Bern, Benfica played with the reserve squad and was defeated 1–4. Eusébio scored a goal and missed a penalty (the first of only five he missed throughout his career), but this was not enough to win the round (4–5 on aggregate). On 10 June 1961, Eusébio played for the first time in the Primeira Divisão, the last match day against Belenenses, where he scored a goal in a 4–0 win. On 15 June, Benfica played the final of the invitational Tournoi de Paris against Pelé's Santos, and in the beginning of the second half, with Benfica down 0–4, Béla Guttmann decided to bring Eusébio from the bench to substitute Santana. Shortly after coming in, Santos reached 0–5. However, between the 63rd and the 80th minute, Eusébio scored 3 goals and suffered a foul inside the penalty area, the penalty taker, José Augusto, failed to score though. The game finished 6–3 for Santos, with Eusébio being on the cover of the famed French sporting newspaper L'Équipe.
His following season was the one where he started to gain global recognition among football fans and critics alike. He scored 12 goals in 17 league matches, and even though the club finished third, they won the Taça de Portugal against Vitória de Setúbal, with Eusébio scoring two goals in the final. In that same season, he won the European Cup, also scoring two goals in the final against Real Madrid in a 5–3 result to Benfica. Due to his fine form during the season, he finished second in the 1962 Ballon d'Or, in his first complete season as a professional. In October 1963, he was selected to represent the FIFA team in the "Golden Anniversary" of The Football Association at Wembley Stadium.
Benfica were also European Cup runners-up in 1963, 1965 and 1968. In the 1968 defeat to the English league champions Manchester United at Wembley Stadium, with the scores 1–1, he came close to winning the game for Benfica in the dying seconds of the game, only to have his shot saved by Alex Stepney. Despite this, and the fact that the English side went on to win 4–1 in extra time, he openly congratulated Stepney for his efforts throughout the game, stopping to applaud Stepney as he threw the ball back into play.
He received a number of individual accolades and awards while playing for Benfica. He was the 1965 European Footballer of the Year (Ballon d'Or) and finished as runner-up twice, in 1962 and 1966, and in 1968 was the first winner of the Golden Boot Award, as Europe's leading scorer, a feat he repeated five years later. He was the Portuguese First Division's top scorer seven times (1964, 1965, 1966, 1967, 1968, 1970 and 1973), helping Benfica to win 11 Primeira Liga (1960–61, 1962–63, 1963–64, 1964–65, 1966–67, 1967–68, 1968–69, 1970–71, 1971–72, 1972–73 and 1974–75), 5 Portuguese Cup wins (1961–62, 1963–64, 1968–69, 1969–70 and 1971–72), 1 European Cup win (1961–62) and 3 European Cup finals (1962–63, 1964–65 and 1967–68).
Eusébio scored 473 goals in 440 official matches for Benfica, including 317 goals in 301 Primeira Liga matches, and 59 goals in 78 matches of UEFA club competitions. Overall, he scored 727 goals in 715 matches wearing Benfica's jersey.