The FA Cup, from this season onwards, began to incorporate a series of qualifying rounds in order to determine qualifiers for the actual Cup competition itself. The qualifying rounds were made up of amateur teams, semi-professional teams, and professional sides not yet associated with the Football League. The only game to be played on Christmas Day took place, Linfield Athletic beating Cliftonville 7–0.^[1] Everton became the first Football League team to withdraw from the Cup after drawing Ulster in the first qualifying round.^[2]

See 1888–89 FA Cup for details of the rounds from the First Round onwards.

• 6 October 1888

1. Ashington 0–4 Elswick Rangers
2. Chester City 2–2 Macclesfield Town – Home team Disqualified
3. Dulwich 0–13 London Caledonians
4. Kettering 3–4 Newark
5. Stoke 1–2 Warwick County
6. Maidenhead 4–0 Old Etonians
7. Rochester 2–4 Old Harrovians
8. Old Wykehamists 1–2 Chatham
9. Notts County 4–1 Eckington Works
10. Old Foresters 2–0 Schorne College
11. Blackburn Olympic W-W Fleetwood Rangers – Walkover Home
12. Sheffield Heeley 6–1 Redcar
13. Grimsby Town 1–1 Lincoln City
14. Clitheroe 3–2 Blackburn Park Road
15. Irwell Springs 4–5 Southport Central
16. Hurst 0–0 Bolton Wanderers
17. Middlesbrough 0–1 Ecclesfield
18. Hartford St John's 1–7 Nantwich
19. Old Brightonians W-W Hendon (1) – Walkover Home
20. Rawtenstall 3–4 Rossendale
21. Casuals W-W Hitchin – Walkover Home
22. Burton Swifts 1–3 Leek
23. Luton Town 4–0 Reading
24. Burton Wanderers 3–0 Wednesbury Old Ath.
25. Lancing Old Boys 4–0 Millwall Rovers
26. Horncastle 2–1 Grantham
27. Chesham 4–2 Lyndhurst
28. Basford Rovers 3–1 Belper Town (1)
29. Crusaders 5–1 Royal Engineers
30. Wellington St George's 1–1 Shrewsbury Town
31. Newcastle West End 7–2 Bishop Auckland Church Inst.
32. Morpeth Harriers 5–0 Whitburn
33. Over Wanderers 1–5 Chester St Oswalds – Home team Disqualified
34. Great Bridge Unity 0–1 Aston Shakespeare
35. Scarborough 2–0 Whitby (1)
36. Newcastle East End 3–1 Port Clarence
37. Park Grange 1–0 Rotherham Swifts
38. Liverpool Stanley 3–0 Workington (1)
39. Heywood Central 2–3 Astley Bridge
40. Birtley 2–0 Darlington
41. Sunderland Albion 8–2 Shankhouse
42. Ulster W-W Everton – Walkover Home
43. Gorton Villa 2–6 West Manchester
44. Beeston St John's 2–0 Notts Olympic
45. Doncaster Rovers 1–9 Rotherham Town
46. Wrexham 3–0 Davenham

Replay

• 13 October 1888

1. Bolton Wanderers W-W Hurst – Walkover Home
2. Lincoln City 1–1 Grimsby Town
3. Shrewsbury Town 2–1 Wellington St George's

• 20 October 1888

1. South Bank 4–0 Sheffield

2nd Replay

• 24 October 1888

1. Grimsby Town 3–1 Lincoln City