The side finished ninth in their inaugural league campaign, and as one of the bottom four teams in the division, they were forced to apply for re-election to return for the following season.

Burnley began the season on 8 September 1888 with a 2–5 defeat away at Preston North End, who went on to be crowned league champions that year.

Alec Brady was the top scorer in the league, with seven goals in 20 appearances.

John Yates became the first Burnley player to be selected for an international match when he was called up to the England squad in March 1889, but despite scoring a hat-trick on his debut, he was never picked for England again.

In the FA Cup, Burnley reached the Second Round before being knocked out by West Bromwich Albion.