Foundation and early years
In 1971, a group of young men learned the rules of the game by watching British soldiers playing football and formed their own team. The first pitch was very simple and small, taking the shape of a square sandy plot of land on the main street near the Clock Roundabout in Al Ain.
In August 1971, the club was officially established, taking its name from that of the city. The founders thought it was necessary to have a permanent headquarters for the club and rented a house on the current Khalifa Road for club meetings. The club's founders took responsibility for all the club's affairs, from planning the stadium to cleaning the club headquarters and washing the . Sheikh Khalifa bin Zayed Al Nahyan was approached for assistance and he provided the club with a permanent headquarters in the Al Jahili district and a Land Rover to serve the club and the team. Al Ain made a successful debut by beating a team made up of British soldiers and went on to play friendly matches against other Abu Dhabi clubs. In 1971, the team played their first match against international opposition when they were defeated 7–1 by the Egyptian club Ismaily in a friendly match for the war effort. In 1971, a group members of the club (Hadher Khalaf Al Muhairi, Saleem Al Khudhrawi, Mohammed Khalaf Al Muhairi and Mahmoud Fadhlullah) broke away and founded Al Tadhamun Club. In 1971, Sheikh Khalifa bin Zayed Al Nahyan provided the club with new headquarters with modern specifications: the Khalifa Stadium in Al Sarooj district. In 1974 Al Ain combined with the breakaway Al Tadhamun, to form the Al Ain Sports Club. The first board of directors of the club was formed after the merger under the chairmanship Mohammed Salem Al Dhaheri.
The founders were Mohammed Saleh Bin Badooh and Khalifa Nasser Al Suwaidi, Saeed Bin Ghannoum Al Hameli, Abdullah Hazzam, Salem Hassan Al Muhairi, Abdullah and Mane'a Ajlan, Abdullah Al Mansouri, Saeed Al Muwaisi, Nasser Dhaen, Abdullah Matar, Juma Al Najem, Ibrahim Al Mahmoud, Ibrahim Rasool and Ali Al Maloud and Ali Bu Majeed, who were the members of the Bahraini group of exchange students, and Ma'moun Abdul Qader, Mahmoud Fadhlullah, Al Fateh Al Talb, Hussain Al Meerghani and Abbas Ali from the Sudanese community working in the UAE.
First titles and Entry to the Football League (1974–1997)
In February 1974,.. the club won its first title, the Abu Dhabi League. On 13 November 1974, Sheikh Khalifa was named honorary president of Al Ain, in recognition of his continuing support for the club. On 21 May 1975, Sheikh Sultan bin Zayed Al Nahyan was elected Chairman of Board of Directors. In 1975, Al Ain won its second Abu Dhabi League In the same year on 21 March 1975, the club played its first UAE President Cup losing 4–5 on penalties in the Round of 16 against Al Shaab after drawing 1–1 in normal time. In 1975–76 season, the team participated for the first time in the UAE Football League, finishing runners-up behind Al Ahli. Al Ain won its first League title in the , after drawing 1–1 with Al Sharjah in the last match. In the following season, they finished runners-up to Al Nasr; Mohieddine Habita was the top scorer with 20 goals. In the 1978–79 season, Al Ain secure third place with 27 points in the league and defeated by Al Sharjah in the President Cup final.
Mohammed Bin Zayed Al Nahyan became president of Al Ain on 19 January 1979. Al Ain won the League again in the and lost the President Cup final to Al Shabab of Dubai. In 1983–84, the team won Joint League Cup and followed with its third League title, becoming the second with Al Ahli to have won the championship three times. The team had the strongest attack with 35 goals, and Ahmed Abdullah, with 20 goals was the joint-winner of the Arab League Golden Boot award for top corer, alongside Al Wasl striker Fahad Khamees. This season was the first season in which foreign players were excluded from the UAE League, a restriction which was opposed by Al Ain. The team were eliminated in the qualifying stages of the 1986 Asian Club Championship. After winning the League title in season, Al Ain failed to win any trophies till 1989 when they won the Federation Cup. In the following year they reached the final of the President Cup, losing to Al Shabab.
The 1992–93 season began with several new signings: Saif Sultan (Ittihad Kalba), Salem Johar (Ajman), Majed Al Owais (Al Thaid), Saeed Juma (Emirates). Al Ain won their fourth League title with three games left to play, after a 5–0 win at Al Khaleej. In the following season, they finished second in the Football League and were runners-up the 1993 UAE Super Cup losing 2–1 against Al Shaab of Sharjah. They also reached the President Cup final but were beaten 1–0 by Al Shabab, failing for the fourth time to win the Cup. In 1994 and 1995, Al Ain lost two President Cup finals, finished second in the , won the 1995 UAE Super Cup and lost out in the Asian Cup Winners' Cup second round to the Kuwaiti team Kazma. In the 1996–97 season, Al Ain were eliminated in the round of 16 of the President Cup by Hatta of Dubai and finished fourth in the Football League.
The Golden Age (1997–2003)
Before the start of the 1997–98 season, the honorary board was formed on 7 June 1997. After this important quantum leap, Al Ain won the . In the following season, they won the President Cup and finished runner-up in the league and secured the third place in their second appearance in Asian Club Championship, after the 1985. Ilie Balaci took charge in 1999. He led them to their sixth , while in the Asian Cup Winners' Cup they were eliminated by Al Jaish on the away goals rule in the first round.
In 2003, Al Ain contested the AFC Champions League competition. In the Group stage they won all three matches, beating Al Hilal of Saudi Arabia, Al Sadd of Qatar and Esteghlal of Iran. In the semi-final they were matched against the Chinese side Dalian Shide over two legs. In the first game, Al Ain won 4–2 at home, with Boubacar Sanogo scoring twice. In the return match in China Al Ain went 4–2 down with six minutes to play but won 7–6 on aggregate after a late goal by Farhad Majidi. The final saw Al Ain face BEC Tero Sasana of Thailand. In the home leg, Al Ain prevailed 2–0 with goals from Salem Johar and . At the Rajamangala Stadium on 11 October, Al Ain were beaten 1–0 by Tero Sasano, but won 2–1 on aggregate to become the first Emirati club to win the Champions League.
New Era (2016–present)
In December 2018, Al Ain which celebrated the 50th year anniversary participating in the 2018 FIFA Club World Cup, representing the host nation as the reigning champions of the UAE Pro-League. Al Ain beat Team Wellington from New Zealand in the first round and Espérance de Tunis of 2018 CAF Champions League champions to enter semifinal. On 18 December 2018, Al Ain defeated Copa Libertadores champions River Plate by penalties hosted in home stadium Hazza Bin Zayed Stadium to enter the final for the first time in team history and became the first Emirati club to reach the decisive match. The final, on 22 December, was lost 4–1 to UEFA Champions League winners Real Madrid at the Zayed Sports City Stadium in Abu Dhabi.