Following the end of World War II and the re-establishment of Czechoslovakia, the club developed into an important force in Czechoslovak football.

Inter Bratislava won the 1. liga in the 2008–2009 season and was supposed to be promoted to the Slovak top flight.

However, financial problems of the club led its owner Ľubomír Chrenko to sell Inter's licence to FK Senica in June 2009.

[2] The senior side was re-established in the 2010–2011 season, playing in the V. liga, i.e. the sixth tier of Slovak football.

In the autumn part of the season 2016/2017 Inter was playing home matches on the stadium in Petržalka on Marie Curie-Skłodowska street (stadium of FC Petržalka akadémia), but in spring 2017 the team moved to the city of Stupava, where the team owners created the training center for Inter.

In the autumn part of the season 2016/2017 Inter was playing home matches on the stadium in Petržalka on Marie Curie-Skłodowska street (stadium of FC Petržalka akadémia), but in spring 2017 the team moved to the city of Stupava, where the team owners created the training center for Inter.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Over the last period there has been a steady increase of young players leaving Inter after a few years of first team football and moving on to play football in leagues of a higher standard, with the German Bundesliga (Vratislav Greško to Leverkusen in 1999), Turkish Süper Lig (Juraj Czinege to Elazığspor in 2003, Roman Kratochvíl to Denizlispor in 2002), Super League Greece (Miroslav Drobňák to Xanthi F.C.

The top transfer was agreed in 2001 when 23years old forward and topscorer Szilárd Németh joined Premier League team Middlesbrough F.C.