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The club was founded on 1 February 1902 as Sportsklubben Thor, but changed its name to Sportsklubben Lyn in 1903. The club had departments for both skiing and speed skating, but these departments left Lyn in 1910 and joined Gjøvik IF together with Gjøvik Skiklubb, Gjøvik Tennisklubb and Gjøvik Turnforening. The club had only their football department left and therefore changed its name to Fotballklubben Lyn. Lyn played its first final in the Norwegian Cup in 1914, but lost the final 2–4 against Frigg. After World War II, Fotballklubben Lyn changed their name to Sportsklubben Gjøvik-Lyn to distinguish themselves from Lyn from Oslo. Gjøvik-Lyn won the 1962 Norwegian Cup after Vard was defeated 2–0 in the final at Ullevaal Stadion on 28 October 1962. As Norwegian Cup winners, Gjøvik-Lyn qualified for the first round of the 1963–64 European Cup Winners' Cup, where they lost 0–7 on aggregate to cypriot side APOEL.

On 15 April 1993, Gjøvik-Lyn was merged with Gjøvik SK. Ahead of the 2009 season, the first team joined the new team Gjøvik FF.

On 23 September 2013, the club decided to merge with Gjøvik FF and change the club's name to Fotballklubben Gjøvik-Lyn, effecting from 1 January 2014.