Before the Isthmian League was formed, there were no leagues in which amateur clubs could compete, only cups. Therefore, a meeting took place between representatives of
Clapton, Ealing Association,
London Caledonians to discuss the creation of a strong amateur league. All the clubs supported the idea and the Isthmian League was born on 8 March 1905. Membership to the league was through invitation only. The league was strongly dedicated to
amateurism; the champions did not even receive a trophy or medals; the league motto was honor sufficit.
Teams less able to compete financially thus gravitated to it rather than the
, while those with ambition and money would move in the opposite direction. Although the league established itself as one of the strongest amateur leagues in the country, routinely providing the winners of the
FA Amateur Cup, it was still seen as being at a lower level than the Southern League which was the top regional
semi-professional league. By 1922 the league had fourteen clubs and over the next five decades, only a few new members were admitted, mainly to fill vacancies left by clubs leaving the league. Most new Isthmian League members joined from the
Athenian League, which was similarly dedicated to amateurism. The Isthmian League was most likely named after the ancient
Isthmian Games, with the later Athenian League,
Delphian League all adding a Classical flavour to amateur football competition.
The league began to admit professionalism in the 1970s. A second division of sixteen clubs was formed in 1973 and a third division followed in 1977. The league refused to participate in the formation of the
Alliance Premier League in 1979 and whilst two Isthmian clubs,
Dagenham, defected to the APL in 1981, it was not until 1985 that the Isthmian League champions were given a promotion place to the newly renamed
. The reward of promotion into the Conference means that, since 1985, no team has retained the title (as had happened on 22 occasions previously). The Athenian League disbanded in 1984 when the Isthmian League Second Division split into North and South Divisions. These were restructured again to Second and Third Divisions in 1991.
In 2002, the league was restructured again, with the First and Second Divisions merging to become Division One North and Division One South, and the Third Division being renamed as Division Two. In addition, the league's three feeder leagues—the
Spartan South Midlands League—ran in parallel with Division Two, and were able to feed directly into the regional Division Ones.
pushed through a major restructuring of the non-league
National League System, creating new regional divisions of the Football Conference. The Isthmian League was reduced back down to three divisions, and its boundaries were changed to remove the overlap with the
In 2006, further reorganisation saw a reversion to two regional Division Ones and the disbandment of Division Two. This current plan calls for clubs based on the edges of the Isthmian League's territory to transfer to and from the Southern League as necessary to maintain numerical balance between the leagues. One team,
Clapton, had been ever-present in the Isthmian League since its foundation, but they moved to the Essex Senior League for the 2006–07 season.
Dulwich Hamlet, who joined the league in 1907, are currently its longest serving member.
The Isthmian League was the first league to have sponsorship, having been selected by
Rothmans, who sponsored the league from 1973 to 1977. The company offered prize money for position in the league but money was deducted for
bookings. Thus the money encouraged both more goals and fair play. The sponsors after Rothmans to the present day have been: Michael Lawrie (1977–78), Berger (1978–82), Servowarm (1982–85),
Diadora (1991–95), ICIS (1995–97) and
Ryman also sponsored the Isthmian Youth League and Isthmian Development League upon their creations in 2007 and 2013 respectively.
 Ryman chairman
Theo Paphitis added to his league sponsorship through his flagship companies.
Robert Dyas became sponsors of the Isthmian League Cup, Isthmian Veterans Cup, Isthmian Disability Cup and Isthmian Youth Play-Off Cup in 2014, and Boux Avenue sponsored the Isthmian Women's Cup from 2014 to 2017.
Becoming the longest running sports sponsorship in UK football, Ryman announced they would be stepping down as sponsors at the end of the 2016–17 season after 20 years.