The Church had its origins in the Armenian Ladies' Patriotic Society, an organization founded in Fresno on May 1, 1892 to "support orphans, ministers, and evangelists in Armenia." In 1913 the Society changed its name to the Women's Benevolent Society and later became known as the Ladies' Aid Society.

On July 25, 1897, 40 men and women met in Major Daniel E. Nicholls's Hall on I Street (now Broadway near Mariposa Streets) and formally organized the First Armenian Presbyterian Church. The Presbytery of Stockton duly enrolled FAPC in fellowship of Presbyterian churches at a meeting in Oakland on October 20, 1897.

The first Session was formed and Reverend Avedis Vartanian, Khachig Michaelian, and Hagop Azhderian were elected as the first ruling elders. The Reverend Lysander Tower Burbank preached the first sermon in the Armenian language and was unanimously elected as the charter pastor of the Church. A native of New Hampshire, Burbank was educated at Williams College in Massachusetts and Union Theological Seminary of New York City. he was a retired missionary of the American Board of Commissioners for Foreign Missions who had served in Turkey.

Reverend Burbank served FAPC for two years and was succeeded by Reverend George Hartotune Filian, a native of Antioch and a graduate of Chicago Theological Seminary. During his three-year ministry, a church building was constructed at the corner of Santa Clara and Fulton Streets. This was the steepled, octagon sanctuary that authors William Saroyan and A.I. Bezzerides attended in their youth.

Upon Reverend Filian's resignation, Caspar Mallarian, Ph.D., a layperson , was invited as pulpit supply for a six-month period. Reverend John Baptist Haygooni, a Baptist minister educated at New York University and Rochester Theological Seminary, became pastor on January 1, 1905 and served until October 1911.

Reverend Mgrdich Hagop Knadjian, a graduate of Central Turkey College at Aintab and Edinburgh Seminary, followed Reverend Haygooni. A prolific writer of books, Reverend Knadjian helped plant sister Armenian Presbyterian Churches in the communities of Kingsburg and Yttem.

Reverend Knadjian resigned in 1922 and was succeeded by Reverend Doctor Garabed Manoog Missirian, a graduate of Central Turkey College at Aintab and Andover Divinity School in Massachusetts. A vigourous, young, and beloved pastor, Dr. Missirian died from a ruptured apendix after serving a mere three years. Following his death, Reverend Misak Aijian supplied the pulpit for nearly a year.

Reverend Vartan Bedros Amirkhanian was then invited to the ministry of FAPC from the Armenian Presbyterian Church of New Jersey. A survivor of the genocide, Reverend Amirkhanian was a graduate of Euphrates College of Harpoot, the Marash Theological Seminary, and did postgraduate work at Hartford Seminary in Connecticut.

Reverend Amirkhanian served the Church for 17 years. During his ministry, the congregation relocated to First Street and Huntington Boulevard and a new, Spanish-style sanctuary was erected at a cost of $50,000. The cornerstone ceremony took place on March 30, 1942, with eight ministers participating. Shortly after the dedication, Reverend Amirkhanian retired and was named Pastor Emeritus.

The Church next called Reverend Arsham Khachadoor Yeramian to its pulpit. Reverend Yeramian was born in Adabazar, in northwest Asia Minor. He received his education at Northeastern University, Boston University, and Princeton Theological Seminary. He ministered to the Church throughout World War II, when more than 100 young men and women from the Church family served in the armed forces of the United States.

Reverend Yeramian resigned in 1954 and was succeeded by Revered Theodore Yacoub Daghlian. A native of Aintab, Reverend Daghlian received his theological training at South Wales Bible College and served as a missionary, pastor, and editor in Egypt. During his ministry, plans for building expansion were initiated and a financial drive began. Reverend Daghlian resigned in 1962 and for two years the Church was served by pulpit supplies, including Doctor Earle Rolston Harvey, a former missionary to China; Reverend William Sutherland, a former missionary to Pakistan; and Reverend Arshag Hussain.

In 1964, the Reverend Varkes Manuel Kassouni was called to the Church from the Armenian Evangelical Church of New York City. A native of Cyprus, Reverend Kassouni was a graduate of Bob Jones University and New York Theological Seminary. During his 12-year ministry, the Church vigorously pursued its expansion program and constructed a new Christian Education Building and Sanctuary. In 1977, Reverend Kassouni accepted a call to serve as Senior Pastor of the United Armenian Congregational Church of Los Angeles. After his departure, Assistant Pastor Theodore D. Lyons, Jr. shepherded the flock through September 1978.

On December 10, 1978, Reverend Bernard Asadoor Guekguezian was installed as tenth pastor of FAPC. A native of Antioch, Reverend Guekguezian graduated from American University of Beirut, the Near East School of Theology, and New York Theological Seminary. He also studied at Fuller Seminary, Pasadena and Clark University, Massachusetts. Reverend Guekguezian served sister Armenian Evangelical churches in Worcester, Massachusetts and Paramus, New Jersey before coming to Fresno.

With the assistance of Associate Pastors David C. Hammelmann and Gregory V. Haroutunian, Reverend Guekguezian emphasized outreach efforts to native Californians of Armenian descent as well as émigrés from the Middle East and the Republic of Armenia. He retired in January 2001, after presiding over construction of a new Fellowship Hall and celebration of the Congregation’s Centennial. His 22 years of service constitute the longest pastor tenure in FAPC history. In the autumn of 2002, the Session and the Presbytery of San Joaquin conferred the title of “Pastor Emeritus” upon Reverend Guekguezian.

After Associate Pastor Haroutunian resigned, the Congregation called Reverend Samuel Albarian of San Francisco as Associate Pastor. A native of Beirut, Reverend Albarian grew up in Montreal, Quebec and received his divinity training at Talbot Theological Seminary. He came to FAPC from the Associate Pastorship of Calvary Armenian Congregational Church in San Francisco.

In the three years following Reverend Guekguezian’s retirement, Reverend Doctor Lee Allison Hicks and Reverend Louis Robert Paradise served as Interim Senior Pastors to the congregation. Both had served sister churches in the Presbyterian of San Joaquin before coming to FAPC. On June 1, 2003, the congregation called Reverend Mgrdich Melkonian as its 11th Senior Pastor. A native of Aleppo, Syria, Reverend Melkonian was educated at Haigazian University and the Near East School of Theology. After serving as a Christian Educator in the Middle East, he became Senior Pastor of the First Armenian Evangelical Church of Montreal and then Associate Pastor for Parish Development at the United Armenian Congregational Church of Los Angeles, Reverend Melkonian was installed in the Senior Pastorate of FAPC on Sunday, September 21, 2003.