The Anglican Church had its first presence in Honduras as early as the 17th century when English traders, adventurers, and Buccaneers arrived on its soil to exploit the precious woods that made up its tropical forests.  However, it was not until the 20th century that the Episcopal Church established Chaplaincies to serve the employees and their families of the fruit companies such as United, Standard, and Cuyamel Fruit Company.

The first Episcopal Church in Honduras, Emmanuel Church by the Sea, was founded in the Bay Island of Roatan.  Eventually the church spread to the mainland in Trujillo, Colón in 1827, where the St. Paul Mission founded.  The donation of a Bible for the pulpit, was received from the ladies A and D Salisbury and e. a. Hobbard Lady.  This Bible is now the oldest English-language bible that exists in Honduras.

Subsequently churches were founded throughout Honduras including St. John’s Episcopal Church in Puerto Cortes, also named after the Cathedral of St. John Baptist, in Belize City, Holy Trinity Church in La Ceiba, and Holy Spirit in the city of Tela. These last three churches were subsequently maintained by lay readers from the Afro-Honduran Community who were Afro-Caribbean descendants of those who came to build the Panama Canal and the railroads throughout the Caribbean coast of Central America for United Fruit Company in the 19th and 20th centuries. 

Honduras was part of the Diocese of Belize until 1953, when it was transferred to the Protestant Episcopal Church of the United States of America.  In 1957 the Bishop David Richards, was consecrated as first bishop of the province of Central America, which includes countries such as Costa Rica, Honduras, Guatemala, El Salvador, and Nicaragua. It was in the year of 1967, when Bishop William Frey was consecrated Bishop of Guatemala and was placed in charge of the Church of Honduras.  He was expelled from Guatemala in 1971 for his opposition to the political violence in that country.

In 1968 the Diocese of Honduras was formed with a total of four congregations; Holy Spirit in Tela, St. John’s the Baptist in Puerto Cortes, Holy Trinity in La Ceiba and Emmanuel by the Sea in Roatan.

On September 17, 1973 Bishop Anselmo Carral exiled Cuban who was the interim Bishop of Guatemala and Honduras, was consecrated. In that same year, Bishop Ervine Swift was designated to travel to Honduras to investigate whether there were mission opportunities in Honduras and it was concluded that it was feasible.

Two years later, Bishop Hugo Luis Pina, (born in Cuba in 1938), was appointed "missionary in charge" of the Honduran Episcopal Church, establishing his residence in the city of Tegucigalpa.  In 1977 he was elected Bishop of Honduras and was consecrated on June 11, 1978 as the first resident Bishop of the Diocese of Honduras.  He served until 1980.  An important point in the diocese’s history is that it was not until August 24, 1978 that the first Honduran born priest was ordained, the Rev. Albert E. Brooks.

Bishop Leopold Frade was elected and consecrated Bishop of Honduras on January 25, 1984 and served until September 15, 2000.  With the departure of Bishop Frade, Bishop James H. Ottley served as interim Bishop until the Church could elect a new Bishop.  On June 30, 2001, through democratic elections, the Episcopal Church of Honduras elected Rev. Lloyd Emmanuel Allen, as the first native Honduran Bishop in the history of the Church.  Bishop Allen was consecrated on October 20, 2001 and continues to serve to this day.

During Bishop Allen’s tenure the Honduran Episcopal Church, has undergone major changes and growth.  As a mission diocese, the Episcopal Church of Honduras has though out its history remained reliant on the US Episcopal Church.  Upon becoming taking office, Bishop Allen began to immediately encourage the Honduras church to aspire to become a self-sufficient diocese.  As such the diocese undertook a campaign “Self-Sufficiency 2019” to become a fully self-sufficient diocese by 2019.  From 98% dependency on the US Episcopal Church in 2001 to less than 50% in 2014, progress is being made.  This is being done through supporting the individual parishes with micro-finance and business opportunities that will support the work of the church.

In addition to the 156 Episcopal parishes, the diocese is ministering to the nation through its seven bi-lingual schools; the El Hogar farm school, technical school, girl’s boarding school, orphanage; 3 HIV clinics; Anglidesh an organization for the development of Honduras through micro-business finance; and the Faith, Hope, and Joy Housing Project.

Today, the Church is subdivided into two (2) regions (North-Western and Central-South-East) with (10) deaneries.