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Lyn was founded on 3 March 1896 at St. Hanshaugen. Lyn was one of three clubs who in 1902 founded the Football Association of Norway, and is the only one still existing. In the first decade of Football in Norway, the club was one of the strongest and won four consecutive Norwegian Cups from 1908 until 1911. At the 1936 Summer Olympics, six Lyn-players, Arne Brustad, Øivind Holmsen, Fredrik Horn, Magnar Isaksen, Jørgen Juve and Frithjof Ulleberg, represented the Norway national football team that won the bronze medal, with Juve as the team's captain. Jørgen Juve is still the player with the most goals scored for the Norway national team.

Lyn also won the cup in 1945 and 1946 but had to wait until 1964 for their first league-title. With Harald Berg and Ola Dybwad-Olsen as main contributors the club secured another victory in the cup in 1967, and in 1968 the club won The Double, clinching both the League title and the Cup, and became the first team from Norway to reach the quarter-final of the European Cup Winners' Cup, where they met Barcelona. Because of the weather conditions during the winter in Norway, both matches were played in Spain. Lyn lost the first game 2-3 and in the second match Lyn was leading 2–0 with 15 minutes left to play. The match ended 2-2 and thus Lyn was eliminated.

The Double was followed by a dismal period in the club's history. The club was relegated in 1969, and even though the team was promoted back after one year and reached the cup final in 1970, the club was again relegated in 1973. During the next 30 years, Lyn was swiftly relegated and promoted between the first and the third tier and the club was never playing in the top division for more than three consecutive seasons. During this period the fan base eroded and Lyn is said to have lost a generation of supporters.

During the 90s the club went back and forth between the Premier League and the First Division. In 1994, Lyn reached the Norwegian Cup final but lost 2–3 to Molde.

Norwegian investor Atle Brynestad bought the club in 1999, in effect saving it from bankruptcy. In 2000, the team was promoted to the Premier League, after winning the First Division with an unprecedented number of points, and they retained their spot in the top flight the following year. In the 2002-season a strengthened Lyn took the lead early on and had gained a large advantage halfway through the season, but had to settle for a 3rd-place finish after a disastrous slump in form and the controversial appointment of new head coach, Hrvoje Braović. The misery, in part due to the constant hiring and firing of coaches, continued into the next year. Lyn struggled at the bottom of the table for most of the season but avoided relegation thanks to the efforts of team captain Tommy Berntsen, who took on the role as coach after Teitur Thordarson, the 5th coach in two years, had resigned. 2004 was a recovery year for Lyn, ending the season in 6th place and reaching the Norwegian Cup final (lost to Brann).

2005 was an eventful year for the club, both on and off the pitch. The club's youth program was beginning to bear fruits and with former international Henning Berg as the new head coach the club claimed 3rd spot in the league. Lyn defeated Rosenborg at Ullevaal for the first time since 1968 and repeated the feat in the away game.

In April, the club's talented Nigerian midfielder Mikel John Obi signed a contract with Manchester United, and according to a statement by Lyn's managing director Morgan Andersen, it was the most expensive transfer in Norwegian football to date. The transfer has since been the source of a heated dispute, and Mikel instead joined Chelsea after a long period of time. FIFA released an announcement stating that Lyn had done everything correct in the process. The transfer is said to have cost Chelsea £16 million. £12 million of this to Manchester United and £4 million to Lyn.

On 10 October 2008, Chelsea announced on their website that they were initiating legal proceedings against Lyn Oslo and their former director Morgan Andersen in an attempt to recover the entire £16 million fee paid. Chelsea maintain that this was due to the contract of the original transfer being based on a fraudulent misrepresentation.

In 2007, the club sold Nigerian international Chinedu Obasi to TSG Hoffenheim for an expected €5 million.

The 2009 season was again very disappointing with the club relegated from Tippeligaen and saved from liquidation at the last moment.

The 2010 season saw Lyn at Bislett Stadium (sharing with Skeid) in the second level of Norway football. In April 2010 Idar Vollvik's company, Ludo, was presented as the club's latest sponsor in an attempt to rescue the club from its financial crisis, but to no avail, and on 30 June 2010, the club declared bankruptcy.

Following the bankruptcy, Lyn's fans gathered around the club's surviving team in the 6. divisjon (seventh tier) for the remainder of the 2010 season moving their home games to Frogner Stadion, drawing large crowds to their home games. In late 2010, Lyn club paid all debt associated with the reserves team of the bankrupt top-flight club. The football association then awarded Lyn the licence formerly held by the reserves, allowing the club to play the 2011 season in the Fourth Division. Led by Finn Bredo Olsen, Lyn secured promotion to the 3. divisjon, after a perfect season with no losses or draws. On 30 September 2012, Lyn secured promotion to the 2. divisjon, after beating Lommedalen 9–0 in front of 2,113 spectators at Frogner Stadion. But, in 2015, Lyn was relegated to the 3. divisjon after three seasons and the unsuccessful attempts to promote to the 1. divisjon. After 6 seasons in the 3. divisjon, Lyn got promoted to the 2. divisjon in 2022. The next season they got promoted to the 1. divisjon for the first time since 2010.