At the beginning of the 20th century Mennonites began homesteading in the western end of the Carrot River Mennonite Reserve. This area became known as Lost River and is in the Rural Municipality of Nipawin (RM487), about 26 kilometers west of the town of Nipawin and south of the Saskatchewan River. By 1906 these Mennonites began to meet in homes for worship; they received visits from a number of pastors. On November 6 & 7, 1913 Ältester Abraham Doerksen of the Manitoba Sommerfeld Church baptized 42 persons and ordained Aron Dörksen and Abram R. Bergen as pastors. In March 1914 a brotherhood meeting (Brüderschaft) decided to build a church; this has been considered the congregation's founding. However, growing differences in the group soon led to a painful division. One group, which included Abram R. Bergen, in 1915 chose to build on the SW quarter, section 30, township 49, range 16 west of 2nd meridian (SW-30-49-16-W2) and affiliated with the Bergthaler Church. The other group which already in 1915 affiliated with the Conference of Mennonites in Canada met on December 6, 1916 at the home of Aron Dörksen and received a proposal to restructure their congregation. Two members of the Committee on Home Missions (Innere Mission) of the Conference of Mennonites in Canada, John Gerbrandt of Drake, Saskatchewan and Gerhard Epp of Eigenheim, Saskatchewan, assisted. By unanimous agreement the group agreed to form the Bethany Mennonite Church, then known by its German name Bethania Mennoniten Gemeind with twenty-seven men and women as founding members.

Aron Dörksen was recognized as the founding pastor of Bethany Mennonite Church. Henry H. Neufeld was elected as treasurer and David H. Neufeld as secretary. The following summer work began on construction, with the completed church dedicated on 8 July 1917. The building was on Aron Dörksen's farm at SE-36-49-17-W2. This is just 2 km north of the Bergthaler church on the west side of the road. In 1926 the building was enlarged by adding 14 feet. By 1945 the growth required a new structure with a basement on the old site. The congregation built a manse in 1960, a porch in 1964 and an extension to the church in 1974. That building burned in 1988, but a new building was constructed in the same year near the old foundation.

In August 1914 Bethany Mennonite Church began Sunday school instruction for the children. In October 1918 the Lost River Ladies Aid was formed. It was later renamed the Bethany Mission Circle and continued until 2011. A second pastor, Jacob J. Enns, was ordained in 1919. Isaac Epp who taught at Two Rivers Bible School was the first pastor to receive payment at a very modest level. Abe Buhler was the first fulltime paid pastor.

From its founding until the 1930s the congregation received regular visits from Reiseprediger of the Conference Home Missions. They performed baptisms and ordinations and encouraged spiritual growth because the congregation was without its own bishop and was isolated from the larger Mennonite communities. At the end of 1939 the congregation purchased a small log building and located it east of Teddington on the Peter Enns farm. At this mission outreach station, Charlie Dirks served as pastor. This outreach included both worship and a Sunday School for the children and continued into the 1950’s.

With the coming of Russian Mennonite immigrants in the 1920s the congregation reached its peak attendance in 1941 with 327 souls, including 170 members. Membership began to decline in the 1950s with the general decline in Saskatchewan's rural population. In the 1940’s the change from German to English occurred gradually and was encouraged by the use of the General Conference Mennonite Church’s English language hymnbook. By the mid 1950s worship services were almost entirely in English.

From its beginning, the congregation affiliated with the Conference of Mennonites in Canada and later with the North American General Conference Mennonite Church and with the Conference of Mennonites of Saskatchewan. Under the leadership of pastor Frank Eidse the congregation withdrew from all Mennonite conference affiliations in 1971. Since then Bethany has operated without any denominational ties, functioning as the local community church and welcoming all who would like to come.