The 1938–39 Northern Football League season was the 46th in the history of the Northern Football League, a football competition in Northern England.
| Competition: | Northern League |
| Season: | 1938–39 |
| Winners: | Bishop Auckland |
| Matches: | 182 |
| Total Goals: | 865 |
| Prevseason: | 1937–38 |
| Nextseason: | 1939–40 |
The league featured 14 clubs which competed in the last season, no new clubs joined the league this season.
Billingham South dropped the ‘South’ part from their name.