The school on Sherkin Island was presented with a prize by the Taoiseach Mr Ahern and Tánaiste Ms Harney for its participation in the logo selection process.
The West Cork students joined thousands voting on a department website for the one they liked best. All the schools and colleges who voted for the winning design were entered in a draw which the Sherkin Island school won.
Six students and two teachers travelled to Dublin to collect their prize of a digital camera. In a reciprocal gesture, the island children presented the Taoiseach with a painting of Sherkin.
Ten-year-old Michael Collins said fellow pupils on Sherkin supported the winning logo for the simplicity of its design.
"When you looked at it you understood what it was," he said. "We undertook a project on Ireland and the EU and we felt that the harp was the symbol for Ireland and the stars a symbol of the EU. Combined they were a perfect representation of Ireland and the EU," he said.
A number of design options had been posted on the website Scoilnet.
The winning entry was submitted by Dublin company Red Dog.
Taoiseach Mr Ahern said it was fitting that young people from all over Ireland were involved in the selection of the logo that will be used on all material relating to the EU Presidency in Ireland.
"The European Union is about people," he said, "and it will continue to have a major impact on the lives of all our young people."
Mary Doherty, managing director of Red Dog, said it was a great honour to have the company's design chosen by young people throughout the country.
"The logo had to be something that people could link immediately to Ireland but yet evoke the atmosphere of a modern, progressive, country," she said.