The 1898–99 season was the fifth in the history of the Southern League. This season saw the expansion of Division One up to 14 teams and creation of Division Two South-West, though it was disbanded at the end of the season after all its clubs left. No Southern League clubs applied for promotion to the Football League.Southampton were Division One champions for the third season in a row. Overall Division Two champions being decided in a playoff in which Thames Ironworks defeated Cowes 3-1 at The Den.
| Competition: | Southern Football League Division One |
| Season: | 1898–99 |
| Winners: | Southampton (3rd title) |
| Promoted: | none |
| Relegated: | Warmley (resigned) Royal Artillery Portsmouth (test match losers) |
| Matches: | 156 |
| Total Goals: | 506 |
| Prevseason: | 1897–98 |
| Nextseason: | 1899–1900 |
A total of 14 teams contest the division, including ten sides from previous season and four new teams.
Teams promoted from 1897-98 Division Two:
Newly elected teams:
| Competition: | Southern Football League Division Two London |
| Season: | 1898–99 |
| Winners: | Thames Ironworks |
| Promoted: | none |
| Relegated: | St Albans (folded) Uxbridge (resigned) |
| Matches: | 132 |
| Total Goals: | 597 |
| Prevseason: | 1897–98 |
| Nextseason: | 1899–1900 |
Division Two London was formed on basis of previous season Division Two. A total of 12 teams contest the division, including eight sides from previous season and four new teams.
Team relegated from Division One:
Newly elected teams:
| Competition: | Southern Football League Division Two South-West |
| Season: | 1898–99 |
| Winners: | Cowes |
| Promoted: | none |
| Relegated: | league disbanded |
| Matches: | 30 |
| Total Goals: | 160 |
| Prevseason: | 1897–98 |
| Nextseason: | 1899–1900 |
Division Two South-West was newly formed and short-lived formation. At the end of the season the division was liquidated and the League returned to 2-division structure.
At the end of the season, test matches were held between the bottom two clubs in Division One and the top club in both Division Twos. Royal Artillery Portsmouth lost 4-1 to Cowes and were relegated to Division Two, whilst Cowes were promoted. Royal Artillery Portsmouth then disbanded.[1] Sheppey United and Thames Ironworks drew 1-1, leading to Sheppey remaining in Division One and Thames Ironworks joining them.