Berisha visited Prague on Tuesday and handed the official application to Mirek Topolanek, the prime minister of the Czech Republic, which holds the EU's rotating presidency.
Albania along with Croatia became NATO members on April 1. Berisha has said EU membership is a key aim for the once-isolated country, which holds parliamentary elections on June 28.
Croatia is already officially recognized as a candidate to join the 27-member bloc, as are Macedonia and Turkey.
EU enlargement commissioner, Olli Rehn, said, however, that Tirana needs to take steps to ensure its parliamentary elections meet international standards before applying for membership.
Albanian Integration Minister Majlinda Bregu said previously that the application should contain details of Albania's democratic achievements and changes introduced in the country.
"As a NATO member, Albania is carrying out reforms and is obliged to conduct free and fair elections that are a necessary condition for EU entry," she said.
Albania has been a parliamentary democracy since 1991 following years of communist-style dictatorship under then leader Enver Hoxha, who died in 1983.
Although Albania is one of the poorest states in Europe, economic growth has helped reduce the number of people living in poverty by a third, according to a study carried out by the World Bank, the United Nations and Albania's statistics institute.
