The 1998–99 Northern Football League season was the 101st in the history of Northern Football League, a football competition in England. Division One was won by Bedlington Terriers and Division Two was won by Durham City. Bedlington opted against promotion to the Northern Premier League. 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.