Mr Higgins spoke about the case with the head of the Coptic Church
President Michael D Higgins says the case of jailed Irish man Ibrahim Halawa needs 'an urgent resolution'.
The mass trial of Mr Halawa was adjourned in Egypt for the 24th time on Wednesday.
He has now spent 45 months in prison, having been arrested and detained in August 2013.
Amnesty International has declared Ibrahim a Prisoner of Conscience.
He was speaking following a meeting with His Holiness Pope Tawadros II, Pope of Alexandria and Patriarch of the See of St Mark.
President Higgins received the Pope at Áras an Uachtaráin on Thursday.
He was accompanied by the Egyptian Ambassador to Ireland, Soha Gendi, the Bishop of the Coptic Diocese of Ireland and other dignitaries.
During their meeting, President Higgins conveyed his condolences on the loss of life following recent attacks on two Coptic churches in Tanta and Alexandria on Palm Sunday.
The pair then went on to discuss a number of issues of national, regional and global importance.
Both leaders stressed the importance of international cooperation based on the rule of law, the realisation of existing international commitments to meet major challenges, and to affirm and strengthen guarantees to human rights and fundamental freedoms.
The leaders emphasised the crucial value of human rights, including the freedom of religion and the rights of prisoners.
President Higgins made particular reference to the case of Irish citizen Ibrahim Halawa, which he described as needing an urgent resolution.
President Higgins and Pope Tawadros II highlighted the importance of inclusive political dialogue in seeking to bring an end to conflict.
They also stressed the urgency of ensuring stability, democracy and sustainable development.