The 1988–89 season was the 74th season of the Isthmian League, which is an English football competition featuring semi-professional and amateur clubs from London, East and South East England.
In the summer of 1988, Oxford City had left the league after losing its ground.
Also in the summer of 1988, Walthamstow Avenue merged into Leytonstone/Ilford: the new club regained Leytonstone/Ilford's name and place in the Premier Division.
At the end of the season Leytonstone/Ilford were refused in promotion due to ground problems.
Farnborough Town finished second and were promoted back to the Conference after four years in the Isthmian League.