The league was formed in 2000. It began as a single division and expanded to include a Division One for the 2005–06 season. Reckitts won the league five times in the first six seasons of its existence.
So far only two clubs – Hull United in 2015  (their stay in the NCEFL was just a single season) and East Yorkshire Carnegie two years later – have taken the step up from this league due to its status as a relatively new league and the general lack of hierarchical football structure in the Yorkshire area.
Barton Town joined the league when it was formed in 2000 but only stayed for one season before they joined the Central Midlands Football League the following season. Barton’s Reserves team joined the league’s first division for the 2017-18 season.
Cleethorpes Town had a three-season stint in the Humber Premier League, from 2006 to 2009-10. In their first season, they won promotion from the first division after finishing 3rd and after two further seasons, playing in the Premier Division, they decided to rejoin the Lincolnshire Football League for the 2010-11 season.