| Season: | 1999–2000 |
| Winners: | Kidderminster Harriers (2nd Football Conference title) |
| Continentalcup1: | Direct promotion |
| Continentalcup2: | Conference League Cup winners |
| Continentalcup3: | FA Trophy winners |
| Continentalcup3 Qualifiers: | Kingstonian (2nd FA Trophy title), 2nd successive |
| League Topscorer: | Justin Jackson (Morecambe), 29 |
| Biggest Home Win: | Rushden & Diamonds – Northwich Victoria 6–0 (29 January 2000) |
| Biggest Away Win: | Hayes – Rushden & Diamonds 0–5 (4 December 1999) |
| Highest Scoring: | Morecambe – Sutton 6–2 (4 December 1999); Telford – Hednesford 6–2 (3 January 2000); Hereford – Doncaster 5–3 (4 September 1999); Hereford – Scarborough 4–4 (2 October 1999); Rushden & Diamonds – Kidderminster 5–3 (21 September 1999); Northwich Victoria – Kettering Town 2–6 (24 April 2000) |
| Matches: | 462 |
| Total Goals: | 1228 |
| Longest Wins: | Kidderminster Harriers, Southport, Stevenage Borough, 6 matches |
| Longest Unbeaten: | Morecambe, 17 matches |
| Longest Losses: | Sutton, 7 matches |
| Highest Attendance: | Kidderminster Harriers v Rushden & Diamonds, 6,250 (8 April 2000) |
| Lowest Attendance: | Sutton v Scarborough, 460 (20 April 2000) |
| Average Attendance: | 1,619 (– 0.47 compared to the previous season) |
| Nextseason: | 2000–01 |
The Football Conference season of 1999–2000 was the twenty-first season of the Football Conference, also known as the Nationwide Conference for sponsorship reasons.
| width=20 | Rank | width=155 | Player | width=155 | Club | width=50 | League | width=50 | FA Cup | width=50 | FA Trophy | width=50 | League Cup | width=50 | Total |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Justin Jackson | Morecambe | 29 | 1 | 1 | 0 | 31 | ||||||||
| 2 | 24 | 0 | 1 | 1 | 26 | ||||||||||
| 3 | 18 | 1 | 2 | 0 | 21 | ||||||||||
| 4 | 17 | ||||||||||||||
| 5 | 15 | 0 | 4 | 0 | 19 | ||||||||||
| 6 | 14 | 1 | 3 | 0 | 18 | ||||||||||
| = | 14 | 1 | 0 | 0 | 15 | ||||||||||
| 8 | 13 | 0 | 2 | 1 | 16 | ||||||||||
| = | 13 | 5 | 0 | 0 | 18 | ||||||||||
| = | 13 | 1 | 1 | 0 | 15 | ||||||||||
| = | 13 | 2 | 0 | 0 | 15 | ||||||||||
| = | 13 | 0 | 2 | 2 | 17 | ||||||||||
| 13 | 12 | 0 | 3 | 2 | 17 | ||||||||||
| = | 12 | 0 | 0 | 0 | 12 | ||||||||||
| = | 12 | 0 | 1 | 1 | 4 | ||||||||||
| = | 12 | 1 | 1 | 0 | 14 | ||||||||||
| = | 12 | 2 | 2 | 1 | 17 | ||||||||||
| = | 12 | 1 | 1 | 0 | 14 | ||||||||||
| = | 12 | 1 | 0 | 0 | 13 | ||||||||||
| 20 | 11 | 2 | 2 | 0 | 15 | ||||||||||
| = | 11 | 0 | 2 | 0 | 13 | ||||||||||
| = | 11 | 0 | 1 | 0 | 12 | ||||||||||
| = | 11 | 2 | 0 | 0 | 13 | ||||||||||
| = | 11 | 0 | 0 | 0 | 11 | ||||||||||
| = | 11 | 0 | 0 | 0 | 11 | ||||||||||
| = | 11 | 0 | 1 | 0 | 12 | ||||||||||