Gibraltar was admitted as a provisional member of UEFA last week, following an earlier decision by the Court of Arbitration for Sport (CAS).
"While noting the grudging nature of the UEFA Executive Committee's decision the GFA greatly welcomes the decision to grant provisional membership of UEFA," a GFA statement said on Tuesday.
"It is unfortunate it has taken so many years and three legal judgements before finally complying with their duties. The GFA hopes it will not take a similar number of years and court cases for it to obtain the full membership it is entitled to."
Gibraltar's application for full membership is set to be discussed at UEFA's Congress in Duesseldorf in January.
UEFA said they had no choice but to allow Gibraltar provisional membership but pointed out that world soccer's governing body FIFA had determined the British territory did not meet their requirements.
"As FIFA knows from the CAS rulings, the FIFA statutes that apply to the GFA's application are those in place between 1997 and 1999, when we met all their statutory requirements," the GFA statement continued.
The GFA also responded to remarks from UEFA's chief executive Lars-Christer Olsson, who said the Executive Committee were not in favour of Gibraltar's full membership as it could have ramifications beyond the disputed territory, which Spain claims sovereignty over.
"The GFA situation is different because our application was made before UEFA statutes were changed (2002). If any application were received from the Basques or Catalans etc in the future, it would not comply with the current statutes and would fail," they said.