The tournament featured teams from the top three levels of the football pyramid. These three levels and 8 leagues, namely the TT Pro League, National Super League, Central FA's Premier Division, Eastern FA's Premier Division, Eastern Counties' Football Union, Northern FA's Premier Division, Southern FA's Premier Division, and Tobago FA's Premier Division, each have their own separate qualification process to trim their ranks down to their final team delegations. The top eight finishers in the Pro League for the 2008 season all qualified for the competition. In addition, the top eight finishers from the Super League also qualified. However, only three clubs from 4 of the 6 regional football associations were awarded qualification into this year's edition, with the Eastern Counties and Northern FA as the exceptions as they only received two. The following clubs qualified for the 79th edition of the FA Trophy:
All matches were played over two 45 minute halves, and in the process if the match were drawn at the end of regulation time, then two additional 15-minute halves were used, and if necessary, penalty kicks if still drawn after extra time.
The draw for the second round took place on 4 December 2008 and involved the 16 winning teams from the first round. These were from the following levels:
Matches in the second round were played on 7 December 2008. 1976 FC Phoenix and WASA provided the Trophy's first two upsets over Pro League clubs by putting out Joe Public and North East Stars, respectively. Another surprise from the round was that Dathea Copious Suns defeated T&TEC to be the lone representative from the third level of the pyramid in the quarterfinals.
Quarterfinals
The draw for the quarterfinals took place on 8 December 2008 and involved the 8 winning teams from the second round. These were from the following levels:
5 from Level 1
2 from Level 2
1 from Level 3
Matches in the quarterfinals were played on 10 December 2008. WASA remained the only club from outside the TT Pro League to advance to the semifinals after defeating Dathea Copious Suns. Caledonia AIA needed extra time to defeat St. Ann's Rangers, Defence Force stunned San Juan Jabloteh 2-1, and W Connection put out giant-killers 1976 FC Phoenix to advance to the semifinals. ---- ---- ---- ----
Semifinals
The draw for the semifinals took place on 11 December 2008. It consisted of Caledonia AIA, Defence Force, and W Connection from the Pro League and WASA from the National Super League. The semifinal matches took place at Marvin Lee Stadium on 15 December 2008. W Connection made quick work of Super League side WASA to end their run in the competition by putting up eight goals. Caledonia AIA defeated Defence Force 4-2 to make it back-to-back final appearances. ---- ----
Final
The final was played at Marvin Lee Stadium in Macoya, Trinidad on 17 December 2008. The match was contested by Caledonia AIA, who beat Defence Force 4-2 in their semifinal, and W Connection who beat WASA 8-1. Caledonia AIA used a goal late from Conrad Smith to level the match at two each in the 82nd minute. After the match ended 2-2 in regulation, Caledonia AIA used the momentum and produced a goal from Jameel Perry in the 108th minute to give Caledonia AIA their first FA Trophy title. Atiba McKnight claimed the title of the Trophy's leading goal scorer with six goals for W Connection on their way to the final.
