The league was established at the end of the 2011–12 season and replaced the Regionalliga Süd at this level in Bavaria.

Many clubs also struggled to cope with the 400-pages long license application, having to rely on volunteers rather than being able draw on permanent staff.

[6] In a special conference of the German Football Association, the DFB, in October 2010, 223 of 253 delegates voted for a reform of the league system on the fourth level.

[2][6] On 16 December 2011, the Bavarian Football Association (German abbreviation: BFV) introduced the league's logo.

[7] In March 2012 the BFV announced that the league champions, apart from having the opportunity to compete in the promotion round to the 3.

[9] The BFV planned to complete the licensing procedure by 20 April 2012 and notify all clubs of the outcome by that date,[7] but this process was delayed.

[10] On 20 April 2012 the FSV Erlangen-Bruck opted to withdraw its Regionalliga application because of ongoing financial issues.

It was later suspended until 31 August, necessitating a cancellation of the 2020–21 season as the BFV approved a resumption of the preceding one with 17 teams after 1 September and its extension to mid-2021.

[13][14] The top goal scorers and spectator statistics for the league are: The first-ever round of the new Regionalliga Bayern kicked off on 19 July 2012 with the opening game held at Bamberg, ending with a 1–0 home victory for FC Eintracht Bamberg against SpVgg Bayern Hof.

[35][36] The league was won by the reserve team of 1860 Munich, while FV Illertissen finished as the best non-reserve side and thereby earned the title of Bavarian amateur champion, which qualified the club for the first round of the German Cup.

The FV Illertissen was, for the second consecutive season the best non reserve side in the league and thereby qualified for the first round of the German Cup again.

At the bottom of the table newly promoted FC Amberg and TSV Rain am Lech were both relegated again.

The biggest home win in the league's history was recorded: 12–0, by FC Augsburg II against SV Seligporten.

Liga relegated four teams starting at the end of the 2018–19 season, the champions of the Regionalliga Nordost, along with their counterparts from the Südwest and West, were promoted directly to the 3.

[47] On that date, the Bundestag delegates voted to grant the Südwest and West champions two direct promotions indefinitely starting in 2021.

A third direct promotion place will be assigned according to a rotation principle among the Regionalliga Nord, Nordost and Bavarian champions.

Schweinfurt were then defeated by TSV Havelse, the Regionalliga Nord champions, who won a place in the 2021–22 3.

The make up of the clubs entering the new Regionalligas from the leagues below was left to the regional football association and not regulated by the DFB.

Liga clubs from the state, SSV Jahn Regensburg, SpVgg Unterhaching or Wacker Burghausen, be relegated at the end of the 2011-12 season, they would directly enter the new Regionalliga Bayern.

As Jahn Regensburg did indeed earn promotion the club's reserve side could have entered the league but finished only third in its Landesliga division and thereby narrowly missed out.

Liga clubs, only the SpVgg Unterhaching considered it necessary to apply for a Regionalliga licence, as both Wacker and Jahn were placed in the top third of the 3.

The top nine clubs from the Bayernliga at the end of the 2011–12 season gained direct entry to the new Regionalliga.

[3][52] Of the eighteen Bayernliga clubs, fifteen applied for a Regionalliga licence, with only Aindling, Gerstofen and Unterhaching II opting not to.

The other two available spots went to FC Augsburg II and Würzburger Kickers, who thereby jumped directly from the sixth to the fourth tier of the league system.

[54][55][56] In December 2011 FV Illertissen, playing in the Oberliga Baden-Württemberg, decided to follow Aschaffenburg's example and switched to the Bavarian league system from the 2012–13 season onwards.

Additionally, the six Landesliga champions and runners-up who failed to qualify for the Regionalliga were also to be grouped in the Bayernliga.