Fr Martin, who is a priest of the Derry diocese, will step down from his role as President of St. Columb's College at the end of August to take up the new position in Maynooth.
46-year old Fr Martin was ordained in 1987 and has degrees in mathematical science from NUI Maynooth, theology from St Patrick's College, Maynooth and an M Phil in School Development from the University of Cambridge.
He ministered in St Eugene's Cathedral and taught mathematics and religious education at St Columb's before becoming the college's president eight years ago.
He has also been a member of the executive committee of the Catholic Heads' Association and of the Northern Ireland Consultative Group which advises the Catholic Trustees on Catholic Education.
Fr Martin has a keen interest in music - his favourites are choral, classical and liturgical music - and is a former secretary of Feis Dhoire Cholmcille.
He has served as director of music at St Eugene's Cathedral, Derry Diocesan Advisor in Sacred Music and was a member of the Irish Episcopal Commission for Music in the Liturgy.
He is also a regular contributor to the "Thought for the Day" slot on BBC Radio Ulster.
Last weekend after his appointment as the bishops' executive secretary was announced, Fr Martin said he looked forward to "working closely with the various departments and agencies in assisting the bishops with their task of proclaiming the Gospel to the people of Ireland".
"In recent years I have been privileged to work with the pupils, staff and parents of St Columb's College".
"I hope to bring to my new role in Maynooth the understanding and skills that I have developed here in Derry" he said.
In his new position Fr Martin will play a pivotal role in facilitating co-operation between the island's 32 bishops and enabling them to function more effectively in their own dioceses.
The Commissions and Agencies of the Conference are based at the Columba Centre in Maynooth.
Fr Martin will be replaced as principal of St Columb's by Mr Sean McGinty – the first lay person to hold the post.
The college recently received a National Training Award for its commitment to staff development and an award for Best Practice in the Public Sector.
Fr Martin’s predecessor as executive secretary to the Bishops' Conference, Fr Aidan O'Boyle, will now return to his native Killala diocese, having served eleven years in Maynooth.
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