The 2006–07 FA Premier Reserve League season was the eighth season of the Premier Reserve League since its establishment. Reigning champions of the Northern Division Manchester United had won two consecutive Northern Premier Reserve League titles and three in total but were looking to become the first side ever to win three years in a row. Reigning champions of the Southern League Tottenham Hotspur were looking to match Derby County and Charlton Athletic by winning two Southern Reserve League titles in a row.
Both failed to meet their objectives, with Bolton Wanderers winning the Northern Division on the final day with a 3–1 home win against Newcastle United, and Reading winning the Southern Division after a 4–0 win away to West Ham United.
The Premier Reserve League Play-off Final to determine the overall winner was contested between the two champions – Bolton and Reading – at the Madejski Stadium, with Reading winning the game 2-0 and being crowned overall reserve champions.
Watford, Charlton and Sheffield United's relegation from the senior league meant that, despite their performances in the reserve league, all three teams were relegated from the Premier Reserve League and replaced by the promoted teams Birmingham, Derby County, and Sunderland for the 2007–08 season.
Reserve League North
| width=30 | Pos | width=200 | Club | width=30 | Pld | width=30 | W | width=30 | D | width=30 | L | width=30 | GF | width=30 | GA | width=30 | GD | width=30 | Pts |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Bolton Wanderers Reserves | 18 | 10 | 3 | 5 | 21 | 16 | +5 | 33 | ||||||||||
| 2 | Manchester United Reserves | 18 | 9 | 4 | 5 | 24 | 17 | +7 | 31 | ||||||||||
| 3 | Middlesbrough Reserves | 18 | 9 | 3 | 6 | 31 | 25 | +6 | 30 | ||||||||||
| 4 | Manchester City Reserves | 18 | 9 | 2 | 7 | 27 | 24 | +3 | 29 | ||||||||||
| 5 | Liverpool Reserves | 18 | 8 | 2 | 8 | 24 | 19 | +5 | 26 | ||||||||||
| 6 | Blackburn Rovers Reserves | 18 | 7 | 5 | 6 | 16 | 15 | +1 | 26 | ||||||||||
| 7 | Sheffield United Reserves | 18 | 8 | 2 | 8 | 23 | 23 | 0 | 26 | ||||||||||
| 8 | Newcastle United Reserves | 18 | 6 | 5 | 7 | 29 | 29 | 0 | 23 | ||||||||||
| 9 | Everton Reserves | 18 | 3 | 7 | 8 | 18 | 25 | −7 | 16 | ||||||||||
| 10 | Wigan Athletic Reserves | 18 | 2 | 5 | 11 | 8 | 28 | −20 | 11 |
Reserve League South
| width=30 | Pos | width=200 | Club | width=30 | Pld | width=30 | W | width=30 | D | width=30 | L | width=30 | GF | width=30 | GA | width=30 | GD | width=30 | Pts |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Reading Reserves | 18 | 12 | 2 | 4 | 45 | 15 | +30 | 38 | ||||||||||
| 2 | Watford Reserves | 18 | 11 | 2 | 5 | 26 | 20 | +6 | 35 | ||||||||||
| 3 | Chelsea Reserves | 18 | 10 | 3 | 5 | 26 | 11 | +15 | 33 | ||||||||||
| 4 | Aston Villa Reserves | 18 | 9 | 3 | 6 | 38 | 26 | +12 | 30 | ||||||||||
| 5 | Tottenham Hotspur Reserves | 18 | 8 | 6 | 4 | 22 | 18 | +4 | 30 | ||||||||||
| 6 | Charlton Athletic Reserves | 18 | 7 | 4 | 7 | 28 | 24 | +4 | 25 | ||||||||||
| 7 | West Ham United Reserves | 18 | 5 | 3 | 10 | 18 | 28 | −10 | 18 | ||||||||||
| 8 | Fulham Reserves | 18 | 4 | 5 | 9 | 16 | 30 | −14 | 17 | ||||||||||
| 9 | Arsenal Reserves | 18 | 4 | 4 | 10 | 15 | 29 | −14 | 16 | ||||||||||
| 10 | Portsmouth Reserves | 18 | 2 | 4 | 12 | 12 | 44 | −33 | 10 |
Pld = Matches played; W = Matches won; D = Matches drawn; L = Matches lost; F = Goals for; A = Goals against; GD = Goal difference; Pts = Points