The Bangor-based indie band, whose debut album Tourist History was named best Irish album of 2010, said on stage last night that they would give their €10,000 winnings to Northern Ireland-based charity Abaana.
Abaana carries out projects in a number of African countries including Uganda, Ghana, Zambia and Tanzania.
The €10,000 prize money was provided by the Irish Music Rights Organisation (IMRO) and the Irish Recorded Music Association (IRMA) and the band were also presented with a specially-commissioned award from Recorded Artists and Performers Ltd (RAAP).
On the night, Two Door Cinema Club performed an acoustic set and were up against fellow nominees Adebisi Shank, The Cast of Cheers, Cathy Dave, Fight Like Apes, Halves, James Vincent McMorrow, O Emperor, Imelda May and Villagers.
Previous winners of the Choice Music Prize include Jape, Adrian Crowley, The Divine Comedy, Super Extra Bonus Party, and Julie Feeney.