The church is the fruit of missionary efforts of the Scottish Free Church. In 1915 John A. Mackay came to Peru to found the Anglo-Peruvian College, today San Andrés College, the most renowned Prot school in Peru. He was followed by Calvin Mackay, who arrived in Lima in 1921 and later settled in Cajamarca. The first church was built there in 1936. The first GenAssy was held in 1963. At the time of union the church had five presbyteries — Amazonas, Cajamarca, Celendin (Cajamarca), Lima, and San Martin — and about 3,000 members. The church used Spanish only.
Another Presb church was planted in Peru in 1936. The principal missionary was the American Alonso D. Hitchcock, who began to work in the area of Ayocucho. A team under the leadership of Homer Emerson, together with Florencio Segura, Simon Izarra, Rafael Yupanqui, Fernando Quicana, and Romulo Saune, engaged in the task of translating the Bible into the Quechua of the area. In 1970 the first GenAssy was held. In 1983 the church had 8,000 members and was organized into two synods (Ayacucho and Selva del Valle Apurimac) and 11 presbyteries. In addition to Spanish, Quechua was in use.