Presbyterian missionaries first visited the Nez Perce Native Americans in the mid-1830s and established a variety of missions to convert the Native Americans to Christianity. These missions taught primarily English and Christian doctrine. Notable missionaries included Henry Spalding, Rev, Cowley, Miss Sue L. McBeth, Miss Kate C. McBeth, and Rev, and George L. Deffenbaugh. The McBeth sisters ordained multiple Nez Perce Ministers including Rev. Archie B. Lawyer, Rev. Robert Williams, Rev. Mark Williams, Rev. James Hines.

The Joint Session of the Nez Perce Presbyterian Churches was established in the 1950s as a way to unite the Presbyterian Churches on the reservation. Both Henry L. Sugden and Rev. Hunter were pastors of the Joint Session in the 1960s, 1970s, and 1980s.

Kamiah First Presbyterian Church (also know as First Indian Presbyterian Church) was founded on Christmas Day, 1871. The church was founded by Presbyterian missionaries and transitioned to be run by Nez Perce pastors. Notable Nez Perce pastors include Rev. Robert Williams, Rev. James Hayes D.D. and Archie B. Lawyer. The current church building was built in 1873 with funds from the U.S. Government. The church bell was cast in New York in 1876. The McBeth sisters were actively involved in the ministry of First Kamiah until 1915 and both Sue and Kate McBeth are buried in the church cemetery. Second Kamiah Presbyterian Church was organized by members of First Kamiah in 1890 with Archie B. Lawyer called as the first pastor.

Second Kamiah Presbyterian Church (also referred to as Second Indian Presbyterian Church) was founded on November 2, 1890 with Rev. Archie B. Lawyer serving as the first pastor. The starting membership was 160, many of whom moved over from First Kamiah Presbyterian Church. The current church building was built in 1919.

In 1907 members of the Lapwai, ID community began to gather in worship. After several years without a building Lapwai First Presbyterian Church was founded in 1909 and first pastored by Rev. B. F. Sewell. The longest serving pastor was Rev. Henry L. Sugden (1956-1964, 1978-1995). In the 1960s Lapwai changed its name from Lapwai First Presbyterian to Lapwai Valley.

The first church service held at Spalding Presbyterian Church took place in 1876. The brick facing was added in 1905 and the church still stands in the Nez Perce National Historical Park. Meadowcreek Presbyterian church was founded on August 7, 1887 by former members of Kamiah First Presbyterian Church. Northfork Presbyterian Church (also know as Ahasahka Presbyterian church) burned down in 2008 and was rebuilt by the congregation. All of these churches are located on the Nez Perce Reservation in Idaho and were a part of the joint session under the care of Rev. Henry Sugden and Rev. Hunter Keen.

The Nez Perce Talmaks camp meetings began in 1897 and were held for the 4th of July as a Christian alternative to secular Independence Day celebrations. The goal was to limit Native American Christians' involvement with "Non-Christian" activities. The Talmaks camp shifted in the following decades to celebrate Nez Perce Christians. Today, Talmaks takes place each summer and commemorates the past and present experiences of Nez Perce Christians.

The original manuscripts of the Nez Perce hymns were written and compiled by John Frank (1878-1950). As a member of the Nez Perce community, Frank served on the elder board for Kamiah First Presbyterian church. Frank translated some of he hymns himself, while others were translated by Rev. Henry Spalding and members of the Nez Perce community.