However, it wasn't until 1889-90 that they competed in a senior competition, joining the Lancashire League upon its formation.

The Blues started well in the Lancashire League, with a series of top six finishes, and claimed the title in great style in 1895/96, winning 22 of their 30 games and scoring 105 goals. A second place finish followed two seasons later, but in 1898-99 the original club was disbanded, and for reasons which are unclear, Nelson were suspended by the Lancashire FA.

The Nelson fans had not helped. There were incidents after the FA Cup defeat at Southport Central where Nelson youths, most of whom were drunk, were accused of disgraceful conduct and using abominable and filthy language. But just a few months after their demise, Nelson were reformed and accepted into the North East Lancashire League.

Despite having difficulty making ends meet, Nelson managed to secure regular mid-table respectability, but eventually the bailiffs were called in, and in 1916 Nelson were forced to close down for the duration of the war.

After reforming near the end of 1918, Nelson embarked upon the most remarkable adventure of their history. The crucial step seems to have been their entry into the Central League. It was not clear that this was the right way forward, as some of the teams in the league were reserve teams of Football League clubs, but the decision was vindicated when, in 1921, the thirteen non-reserve teams of that league were voted into the newly formed Third Division North.