Having initially gained admittance to the Scottish Border League in 1905, they were finally elected member of the Scottish Football League in 1955, where they have played ever since, despite low attendances and frequent financial problems.

Despite losing a good deal of the squad to other clubs in the close season, manager John Coughlin exceeded expectations by rebuilding the team and guiding them to the Third Division championship in 2007 , their first title in 28 years, in a season which also saw a new record for consecutive league wins.

They are one of a handful of teams in the world to play in a national football league other than their own country's, where both countries have their own fully professional competitions. Although three Welsh clubs (Cardiff City, Wrexham, Swansea City) play in the English Football League, the League of Wales is mainly a semi-professional competition.Wellington Phoenix based in Wellington will take the place of the defunct Auckland-based New Zealand Knights as the only New Zealand professional team in the Australian A-League, but the recently-founded New Zealand Football Championship is semi-professional. A similar situation pertains with Toronto FC, which participates in Major League Soccer in the USA, while the Canadian Soccer League is semi-professional. The only other team that meets these criteria is Derry City of Northern Ireland, which played in the Football League of Ireland, the former league of the Republic of Ireland, from 1985 to 2006, and will play in the Republic's new FAI National League from 2007.

The town of Berwick-upon-Tweed is near to the Scottish border and is closer to Edinburgh than to Newcastle upon Tyne. The time (and expense) involved in travelling to away matches against English opposition would be prohibitive for the club. The club also formerly played in the East of Scotland League, which contains other nearby Borders teams, prior to joining the Scottish League.

They aim to field a reserve side in this competition from next season. There is also some controversy over Berwick's identity . Entry into the English Football League would result in a round-trip of almost 1,000 miles should Berwick be faced with playing potential rivals Plymouth Argyle, England's southernmost league team.