Nelson reached the sixth qualifying round of the FA Cup, beating non-League Winsford United before being knocked out of the competition by Coventry City.

Two Nelson records were set during the campaign, although one was later broken; the seven-goal winning margin against Crewe Alexandra was never bettered in Football League matches, while the attendance of 13,500 for the visit of Darlington in April 1925 was the largest ever seen at Seedhill at that time.

Former Scotland international defender David Wilson retired from his player-manager role in the summer of 1924 in order to take up the managerial post full-time.

Centre forward Joe Eddleston, Nelson's top goalscorer in each of the previous three seasons, was retained along with captain Clem Rigg, Welsh half-back Jack Newnes and goalkeeper Harry Abbott.

[3] Scottish forward Mike McCulloch ended his two-year association with the club by joining Chesterfield on a free transfer, while half-back Leigh Collins signed for New Brighton.

[5] Several young players were acquired from local non-League football during the close season, including Ambrose Harris from Briercliffe and Billy Harper, formerly of Feniscowles.

Nelson named the same team for the seventh game in succession for the trip to Tranmere Rovers on 4 October, but the side were beaten for the fourth straight away match thanks to goals from Dixie Dean and Jimmy Moreton.

He scored again in the next match as the team gained their first point of the season away from home, drawing 1–1 at Wigan Borough, who had been Nelson's first ever opponents in the Football League over three years previously.

Despite a tenth goal of the campaign from Eddleston and a penalty kick scored by captain Clem Rigg, the team could only draw with Bradford Park Avenue.

After a two-week break from League football because of the FA Cup, Nelson returned to action with a 4–1 home win over Rotherham County in the only match ever played between the two sides at Seedhill.

[10] On Christmas Day, half-back Ambrose Harris made his first appearance for Nelson as the side beat Chesterfield 1–0 thanks to Bill Ellerington's first goal for the club.

Clem Rigg scored two penalties the following week as the side beat Barrow to move above Bradford Park Avenue into fifth position in the Third Division North.

Left-half Herbert Butterworth made his senior debut for the club against Tranmere, despite signing from Wolverhampton Wanderers almost two years previously,[12] while Chadwick scored twice in one game for the first time.

[7] A trip to Walsall seven days later brought a first away victory of 1925 for the team as goals from Chadwick and Hoad gave Nelson a 2–1 win, which elevated them to third place in the league.

[7] Nelson carried their good form into March; Bottrill scored for the first time in over two months to help the team defeat New Brighton by five clear goals.

However, the team suffered their first loss of 1925 in of the following match away at Grimsby Town as goals from Joe Cooper and Frank McKenna gave the home side a 2–0 win.

Joe Eddleston opened the scoring and went on to net his third hat-trick of the season, taking his tally of goals to 25, a total that would never be beaten during Nelson's time in the League.

The 1924–25 season ended with consecutive away losses at Durham City and bottom-of-the-league Rotherham County, leaving Nelson with second in the Third Division North on 53 points, ahead of third-placed New Brighton on goal average.

Nelson won the first ever meeting between the two clubs 4–1 with goals from Braidwood, Eddleston, O'Beirne and Wolstenholme, to progress to the sixth qualifying round for the first time in three years.

Joe Eddleston missed just one game, the defeat against Durham City on 29 April, while Welsh international Jack Newnes made 42 appearances in the season.