During World War I (1915-1918), one and a half million Armenians were massacred by the Turks. In 1921, when the French forces evacuated Cilicia, a second wave of massacres ordered by Kemalist Turkey took the lives of another three hundred thousand Armenians. The rest of the Armenians were forced to leave their homeland and found refuge mostly in Syria and Lebanon. The Catholicosate in Sis was robbed and ruined by the Turks. Catholicos Sahak II followed his flock in exile.

After wandering in Syria and Lebanon, in 1930, he established the Catholicosate in Antelias, Lebanon. Thus, a new era opened in the history of the Catholicosate with the organization of Dioceses and the founding of a new theological seminary. The Armenian people spread all over the world looked at the Catholicosate with new hopes and expectations.

In order to fulfill the great task now entrusted to the Armenian Catholicosate of Cilicia in the Armenian Diaspora, Catholicos Sahak II, already advanced in age, asked the help of Archbishop Papken Gulesserian, who was enthroned as Coadjutor-Catholicos in 1931. Soon a printing press was established in Antelias, a monthly review under the name of HASK (Ear of Corn) started to get published regularly, together with a number of religious, educational, historical and philological publications. The Coadjutor-Catholicos Papken I passed away in 1936, after five years of intensive and fruitful activities.

Archbishop Bedros Saradjian, Primate of the Armenians in Cyprus, was nominated Vicar-General to Catholicos Sahak II. By the donation of Simon and Mathilde Kayekjian, the property of the Catholicosate was purchased from the American Near East Relief organization, which 1922-1928 had run an Armenian orphanage in the same place where the Catholicosate was located in 1930. The Cathedral was built through the donation of an unknown benefactor, whose name, Sarkis Kenadjian, was announced only after his death. A Chapel in memory of the one and a half million Armenian martyrs, as well as a residence for the Catholicos and a new Seminary building were constructed one after the other. Catholicos Sahak died in 1939. He was succeeded by Catholicos Bedros I, who passed away the following year.

The election of the new Catholicos took place in 1943 and the Primate of the Armenian Church in North America, Archbishop Karekin Hovsepiantz, was elected Catholicos. During his pontificate (1945-1952), the Catholicosate flourished primarily in the area of cultural activities. Catholicos Karekin I, being a great scholar, encouraged the higher studies in the Seminary and gave impetus to Armenological publications and conferences. The scope of the work of the Catholicosate was considerably widened.

Four years elapsed between his death and the election of his successor, Catholicos Zareh I Payaslian (1956-1963), the first graduate of the Seminary of Antelias. Catholicos Zareh I was an experienced church leader, having served as Primate of Aleppo (Syria) for sixteen years. During his short reign, the service of the Catholicosate was extended to various communities in the Diaspora who had been in desperate need of spiritual care for many years and the Seminary was given particular attention. His personal insights and saintly life had a determining influence on all and especially the seminarians who entered the service of the Church. The relations of the Catholicosate with other churches and states of the Middle East were strengthened. In 1962, the Catholicosate became a full member of the World Council of Churches and sent observers to the Vatican Council II. His close associate, Archbishop Khoren I Paroyan, the Primate of the Armenian Church in Lebanon, succeeded him in 1963.

Under the pontificate of Khoren I, the Catholicosate went through an era of achievements in various domains. Through his strenuous efforts the Catholicosate reached financial stability; the terrain of the Catholicosate was expanded and new constructions came to meet the growing needs of the Catholicosate. In 1977, Catholicos Khoren wished to have an assistant him.

Archbishop Karekin II Sarkissian, the Primate of the Eastern Prelacy of the USA, was elected Coadjutor-Catholicos. Although 18 years of his pontificate were difficult years in Lebanon because of the civil war, Catholicos Karekin II succeeded to elevate the Catholicosate of Cilicia to a new level of witness and service. He improved the printing house, restarted the publication of the annual "HASK Armenological", established the Christian Education Department, organized seminars on contemporary issues, and enlarged the scope of the ecumenical involvement of the Catholicosate. In April 1995 Catholicos Karekin II was elected Catholicos of All Armenians in Etchmiadzin, Armenia. 

In 1995, Archbishop Aram Keshishian, the Primate of the Armenian Church in Lebanon, was elected Catholicos by an Electoral Assembly composed of 185 clergy and lay delegates.

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