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Football was introduced to Seychelles in the 1930s. Its first official competition, the Challenge Cup, was organized in 1936. Then in 1941, a championship between five teams was set up with matches of 60 minutes, played barefoot.

In 1969, the president of the Seychelles Football Federation wanted to set up a national team. Engaged on a voluntary basis, Adrian Fisher arrived on the island in September to reorganize Seychelles football. He equipped all the players with shoes, introduced contemporary training techniques and extended the match time to 90 minutes. The newly-formed national team played their first matches at a friendly tournament in Kenya in April 1970. In Seychelles' first matches played on a real football pitch, they drew 2–2 against Feisal F.C. then lost 1–2 to Mwengi at Mombasa Municipal Stadium. When Fisher left Seychelles in 1973, the team had played six games against four clubs.

Seychelles played their first match against another national team on March 13, 1974, against Réunion. In this friendly match, the Pirates lost 0–2. Two years later, this time as an independent nation, the Seychelles faced Réunion again, losing 1–4. In September 1977, they played their first match against a FIFA-affiliated team, Mauritius, during a tournament played in Réunion, and lost 1–2. The team enjoyed its first victory the following year by beating Réunion 1–0 at home.

In 1979, Seychelles played their first tournament, the 1979 Indian Ocean Games. They lost their first game 3–0 to Réunion, and beat Maldives 9–0 in their second. In the semi-final, they knocked out Mauritius 4–2 on penalties after a 1–1 draw, but in the final they lost 2–1 to Réunion.

Seychelles were eliminated from the group stage at the 1985 Indian Ocean Games but, on August 31, 1986, they played their first competitive match recognised by FIFA and CAF, following their affiliation with both organisations, a qualification match against Mauritius for the 1987 All-Africa Games, which they lost 1–2. They participated, for the first time, in the 1988 African Cup of Nations qualifiers against Mauritius but lost 1–3 over the two legs.

At the 1990 Indian Ocean Games, the team suffered the heaviest defeat in its history against Madagascar in the semi-final, losing 0–6. In the bronze medal match, they won against Comoros 3–1. Despite hosting the following games, the team failed to repeat this performance, losing all four games and finishing last in the competition.

After the elimination from the preliminary phase of the 1996 African Cup of Nations by Mauritius 2–1 over the two legs, Vojo Gardašević was hired to lead the team. Following that, the Pirates again finished third in the 1998 Indian Ocean Games and, two years later, competed in the World Cup qualifiers for the first time. Playing against Namibia they drew 1–1 in Stade Linité, thanks to a goal by Philip Zialor but lost the second leg 0–3. Seychelles were also eliminated in the preliminary round of the 2000 African Cup of Nations by Zimbabwe 0–6 over the two matches. Seychelles fared better in the qualification for the 2004 African Cup of Nations as the team, led by Dominique Bathenay then Michael Nees, finished third and recorded two prestigious home wins: beating Eritrea 1–0 with a goal by veteran Roddy Victor, and beating a Peter Ndlovu-led Zimbabwe team 2–1 with goals by strikers Alpha Baldé and Philip Zialor. Following that they achieved a bronze medal at the 2003 Indian Ocean Games, then were eliminated in the preliminary round of the 2006 World Cup by Zambia, 1–5 in the two games.

In 2011, Seychelles hosted the 2011 Indian Ocean Island Games and won the tournament for the first time, beating Mauritius in the final on penalties.

The rest of the 2010s saw little success for The Pirates with the high point achieved during 2017 Africa Cup of Nations qualification where they managed a 2–0 win over Lesotho and a 1–1 draw with Ethiopia to finish third in their four-team group.^[]