In 1982, he completed a course in spirituality in the United States.
He is the fourth and current Archbishop of Nairobi, having previously served as Coadjutor Archbishop of Nyeri (2002–2007) and Bishop of Embu (1986–2002). He was elevated to the cardinalate in 2007. He was baptized in 1948, and entered the minor seminary in Nkubu in 1962.
From 1967 to 1974, he furthered his studies in Rome at the Pontifical Urbaniana University (where he obtained a licentiate in philosophy) and Pontifical Lateran University (licentiate in pastoral theology).
On 6 January 1973, Njue was ordained to the priesthood by Pope Paul VI in Saint Peter"s Basilica. Returning to Kenya in October 1974, he did pastoral work in Kariakomu in the southern district of Meru.
He also taught philosophy at the National Seminary of Bungoma, of which he later served as rector from 1978 to 1982. He then served as a parish priest in Chuka and rector of the Philosophical Seminary of Meru.
On 9 June 1986, Njue was appointed Bishop of Embu by Pope John Paul World War II He received his episcopal consecration on the following 20 September from Jozef Cardinal Tomko, the co-consecrators being Bishops Silas Silvius Njiru and Raphael Ndingi Mwana"a Nzeki.
He served as President of the Kenyan Episcopal Conference from 1997 to 2003, and was named Coadjutor Archbishop of Nyeri on 23 January 2002. Following the murder of Bishop Luigi Locati, he served as Apostolic Administrator of Isolo from 2005-2006. Njue was appointed Archbishop of Nairobi on 6 October 2007, and was installed on the following 1 November.
Shortly afterwards, he was created Cardinal-Priest of Preziosissimo Sangue di Nostro Signore Gesù Cristo by Pope Benedict XVI in the consistory of 24 November 2007.
Cardinal Njue serves as Vice President of the International Catholic Migration Commission. During a Holy Thursday Mass the Cardinal was celebrating at Nairobi"s Holy Family Basilica on 28 March 2013, he appealed for calm and peace during the upcoming Easter season as the Supreme Court of Kenya prepares to announce its verdict in the disputed initial round of the presidential election 4 March between Uhuru Kenyatta and Kenya"s Prime Minister Raila Odinga (the decision is expected on Saturday, 30 December).
Kenyatta and Deputy President-elect William Ruto are facing charges at the International Criminal Court (Interstate Commerce Commission) at The Hague that they instigated post-electoral violence in Kenya after the 2007 election. He was one of the cardinal electors who participated in the 2013 papal conclave that elected Pope Francis.
Abortion Gay rights.
Njue has issued a pastoral letter calling abortion a "foreign concept" and blasting the government for attempting to legalise it in Kenya.
In June 2013, after United States president Barack Obama, whose father was Kenyan, said during an official visit in Senegal that African governments should follow the United States example in taking action on gay rights, John Njue replied "Let him forget, forget and forget", based on his view that the United States have "ruined their own societies" and that he does not "think God was making a mistake when he created Adam and Eve".
On 29 December 2011 he was appointed a member of the Pontifical Council for Social Communications for a five-year renewable term. On Saturday, 30 November 2013, Cardinal Njue was named a Member of the Congregation for Catholic Education by Pope Francis.