The club was founded in 1965 by the players who represented Nagano Prefecture. The players frequented a cafe called Yamaga in front of Matsumoto railway station and initially they were simply called Yamaga Club. In 2004, they were renamed as Matsumoto Yamaga FC when nonprofit organisation Alwin Sports Project were set up to support the club with the intention of promotion to J. League. The very coffee shop where they founded the club no longer exists, but the club opened a new one in 2017.

In the 2007 and 2008 season they finished respectively 1st and 4th in the Hokushin'etsu First Division, but failed to gain the promotion to the Japan Football League as they exited at the group stage of the Regional League promotion series against other regional champions. 2008 also brought a crucial Emperor's Cup run, where they defeated former Japanese champions Shonan Bellmare in the third round by penalty kicks, only to be eliminated 8–0 by Vissel Kobe.

The 2009 season brought inconsistency, as they took 4th place in the regional league but knocked Urawa Red Diamonds out of the Emperor's Cup in the second round, their biggest giant-killing ever.

By virtue of winning the Shakaijin Cup, they earned a berth in the Regional League promotion series, and won the series at home to earn promotion to the Japan Football League for 2010. They earned 7th place on their first season in the third tier.

In 2011, despite a season thrown off by the Tōhoku earthquake and tsunami and the resulting inability of Sony Sendai to play a full schedule, Yamaga earned 4th place and were promoted to J. League Division 2. After three seasons they earned their first ever promotion to J1 League, only to be relegated after one season.

After failing to secure promotion in 2016 and 2017, Yamaga finished their 2018 season at the top of the J2 table, winning their first ever league title and securing automatic promotion to J1 in the process.

This began the downfall of Matsumoto Yamaga FC, due to the club's bad idea of high player turnover. Ahead of the 2020 J2 League, Yamaga turned over more than 20 players, in which began a slow start in 2020, as the club also went through many winless runs, including 5 losses in a row, which at the time was a record number of defeats for the club in J2. Eventually, in September 2020, manager Keiichiro Nuno was sacked, and the club finished 13th that season. Things were about to get worse as they continued high player turnover, with twenty-seven players leaving and twenty-four coming to the club before the 2021 J2 League. In June that year, Nuno's replacement, Kei Shibata, was fired from the club, and was replaced with Hiroshi Nanami, who couldn't help the club escape relegation after finishing dead last that season.^[1]

In 2022, Matsumoto played its first season on the J3. Matsumoto failed to be promoted back to the J2 League, as it finished on fourth place in the final standings of the 2022 J3 League season. The club ended tied on points with Kagoshima United, with both having earned 66 points in 34 matches. However, the goal difference stood out in Kagoshima's favour. The club will play its third consecutive season at the J3 during 2024.

The biggest rival of Matsumoto Yamaga are the prefectural neighbours and former Hokushin'etsu League fellows Nagano Parceiro. Matches between those teams are labelled "Shinshū derby" and generate a lot of interest in both cities.^[2] For 2011 season, Parceiro joined their rivals in JFL bringing the derby to the national level.

Matsumoto Yamaga's home ground is Matsumoto Stadium (popularly known as Alwin) located in the Kambayashi area of Matsumoto city. The stadium has a capacity of 20,000 (16,000 seats and 4,000 standings).^[3] It is the third largest Sport venue in Nagano Prefecture.

The mascot of the club is named "Gans-kun" (ガンズくん), who is a Ptarmigan (ターミガン, Tāmigan), the symbol bird of Nagano Prefecture.^[4]

The club's theme song is "wanna be a superstar" by local rock band ASIAN2.^{[citation needed]}

•   Geylang International (2016–present)^[5]

On 23 November 2016, Matsumoto Yamaga and Geylang International signed a Memorandum of Understanding (MOU) in a press event which was held at the Marina Bay Floating Platform. This MOU will enable both clubs to establish a platform to exchange expertise and knowledge with the objective of promoting cohesion and development of football between the two clubs. The MOU spells out possible areas of collaboration such as the exchange of players and technical staff for training attachments and loans. Geylang will be looking to select promising players from its Active SG-GIFC Soccer Academy and junior teams to send on short training stints with Matsumoto Yamaga while the Japanese club is also looking into the possibility of sending players from their junior team to Singapore for pre-season training stints. Amongst the key initiatives of the partnership with Matsumoto Yamaga is the exchange programmes for head coach, Mohd Noor Ali, who had a one-year attachment with the club in 2018, where he guided the club U18 B team to the Japan FA's Under-18 Football League Nagano prefecture title while on 17 August 2018, Anders Aplin become the first Singaporean football player to sign for a J.League team signing on loan until the end of the 2018 J2 League season in November.

On 30 October 2022, both clubs reaffirmed their close and long-standing relationship as Geylang International officials went to Japan to explore future collaborations going into the seventh year of partnership since 2016. Geylang International has a memorandum of understanding with J.League outfits, Matsumoto Yamaga that was signed in 2016, while Epson's relationship with the club also dates back to the same year when it became the club's platinum sponsor. In the last seven years, Epson has enjoyed premium hospitality access to the club's home matches and has also supported the Singaporean football community and youths with the staging of the Epson Youth Cup.

Key

As of 7 February 2024.^[6]

Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

Out on loan edit

Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

• Official website (in Japanese)