The 1989–90 North West Counties Football League season was the eighth in the history of the North West Counties Football League, a football competition in England. Teams were divided into two divisions: Division One and Division Two.
| Competition: | North West Counties Football League Division One |
| Season: | 1989–90 |
| Winners: | Warrington Town |
| Promoted: | Warrington Town |
| Relegated: | Burscough Chadderton |
| Matches: | 306 |
| Total Goals: | 877 |
| Prevseason: | 1988–89 |
| Nextseason: | 1990–91 |
Division One featured three new teams:
| Competition: | North West Counties Football League Division Two |
| Season: | 1989–90 |
| Winners: | Maine Road |
| Promoted: | Bacup Borough Maine Road |
| Relegated: | None |
| Matches: | 240 |
| Total Goals: | 774 |
| Prevseason: | 1988–89 |
| Nextseason: | 1990–91 |
Daisy Hill changed their name to Westhoughton Town
Division Two featured one new team: