The 1998–99 season was the 84th season of the Isthmian League, which is an English football competition featuring semi-professional and amateur clubs from London, East and South East England.
Bishop's Stortford and Bromley finished bottom of the table and relegated to Division One, while Carshalton Athletic were reprieved after Wealdstone, finished third in Division One, were refused promotion due to ground grading.
Molesey, Wembley and Berkhamsted Town relegated to Division Two.
Puma Full Members Cup: Featuring teams from the top two divisions.
Vandanel Trophy: Featuring teams from the bottom two divisions.