[1] Two more clubs, Brierley Hill & Withymoor and Stapenhill, folded after the draws for the early rounds were made, giving their opponents a walkover.

The competition started on 16 August 2008 with the Extra preliminary round and concluded on 30 May 2009 with the Final, held at Wembley Stadium.

Premier League side Portsmouth were the defending champions, but were elimated in the fourth round by Swansea City.

This season's competition saw the beginning of a new television contract for the tournament, with ITV and Setanta Sports taking over the domestic rights from the BBC and Sky Sports, however this would prove to be the only season in which Setanta broadcast the competition, as it went into administration and closed down a few weeks after the final.

These 20 teams came from the following levels: The matches were played between 2 and 5 January 2009, with the exception of the ties between Birmingham City and Wolverhampton Wanderers, Histon and Swansea City, Cheltenham Town and Doncaster Rovers, and Leyton Orient and Sheffield United, which were postponed until 13 January 2009.

It comprised teams from the following levels: The draw was conducted by Roberto Di Matteo and Dave Beasant.

[23] A technical error during ITV's broadcast of the Everton–Liverpool replay meant that millions of viewers missed Dan Gosling's winner for Everton late in extra time.

Coverage of the match was temporarily interrupted by advertisements, only for viewers to see Everton's players celebrating upon the restoration of the feed.

The matches shown live on Setanta Sports were: • Leeds United 1-1 Northampton Town (R1) • AFC Wimbledon 1-4 Wycombe Wanderers (R1) • Tranmere Rovers 1-0 Accrington Stanley (R1 Replay) • Northampton Town 2-5 Leeds United (R1 Replay) • Barrow 2-1 Brentford (R2) • AFC Bournemouth 0-0 Blyth Spartans (R2) • Kettering Town 2-1 Notts County (R2 Replay) • Blyth Spartans 1-0 AFC Bournemouth (R2 Replay) • Tottenham Hotspur 3-1 Wigan Athletic (R3) • Southampton 0-3 Manchester United (R3) • Blyth Spartans 0-1 Blackburn Rovers (R3) • Bristol City 0-2 Portsmouth (R3 Replay) • Derby County 1-1 Nottingham Forest (R4) • Cardiff City 0-0 Arsenal (R4) • Liverpool 1-1 Everton (R4) • Arsenal 4-0 Cardiff City (R4 Replay) • Watford 1-3 Chelsea (R5) • Everton 3-1 Aston Villa (R5) • Arsenal 3-0 Burnley (R5) • Hull City 2-1 Sheffield United (R5 Replay) • Everton 2-1 Middlesbrough (QF) • Arsenal 2-1 Hull City (QF) • Arsenal 1-2 Chelsea (SF) • Chelsea 2-1 Everton (Final)