| Competition: | North West Counties Football League |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
The 1988–89 North West Counties Football League was the seventh in the history of the North West Counties Football League, a football competition in England. Teams were divided into two divisions.
| Competition: | North West Counties Football League Division One |
| Season: | 1988–89 |
| Winners: | Rossendale United |
| Promoted: | Rossendale United |
| Relegated: | Formby |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
Kirkby Town changed their name to Knowsley United
Division One featured 2 new teams:
| Competition: | North West Counties Football League Division Two |
| Season: | 1988–89 |
| Winners: | Vauxhall Motors |
| Promoted: | Vauxhall Motors Chadderton Nantwich Town |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
Division Two featured 1 new team:
Rossendale United were promoted to the Northern Premier League while Formby were relegated to the Second Division. Ellesmere Port & Neston left the League at the end of the season.
Vauxhall Motors, Chadderton and Nantwich Town were promoted to Division One. Daisy Hill changed their name to Westhoughton Town.