The 2012–13 Northern Counties East Football League season was the 31st in the history of Northern Counties East Football League, a football competition in England.
| Competition: | Northern Counties East Football League Premier Division |
| Season: | 2012–13 |
| Winners: | Scarborough Athletic |
| Promoted: | Scarborough Athletic |
| Relegated: | Hall Road Rangers |
| Biggest Home Win: | Bridlington Town 11–0 Nostell Miners Welfare |
| Biggest Away Win: | Lincoln Moorlands Railway 0–10 Scarborough Athletic |
| Matches: | 462 |
| Total Goals: | 1717 |
| Prevseason: | 2011–12 |
| Nextseason: | 2013–14 |
The Premier Division featured 19 clubs which competed in the previous season, along with three new clubs:
| Competition: | Northern Counties East Football League Division One |
| Season: | 2012–13 |
| Winners: | Albion Sports |
| Promoted: | Albion Sports Athersley Recreation |
| Relegated: | Askern Villa |
| Biggest Home Win: | Louth Town 11–0 Askern Villa |
| Biggest Away Win: | Appleby Frodingham 0–8 Dinnington Town |
| Highest Scoring: | Askern Villa 2–10 Pontefract Collieries |
| Matches: | 462 |
| Total Goals: | 1740 |
| Prevseason: | 2011–12 |
| Nextseason: | 2013–14 |
Division One featured 17 clubs which competed in the previous season, along with five new clubs: