The 1998–99 Northern Football League season was the 101st in the history of the Northern Football League, a football competition for teams in north east England. The first division was won by Bedlington Terriers and division two was won by Durham City. Bedlington opted against promotion to the Northern Premier League.
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The league held two cup competitions. The Northern League Cup, competed for by all Northern League sides, was won by Dunston Federation. They beat Jarrow Roofing 4–1 in the final. The Craven Cup, for division two teams, was won by Ashington defeating Evenwood Town 1–0 in the final.
Division One
Billingham Synthonia, Billingham Town, Newcastle Blue Star, Penrith: Three points deducted Source:
Division Two
Eppleton Colliery Welfare: Six points deducted Source:
Craven Cup
For Division Two teams