St. Stephen's Lutheran Church was incorporated in May 1964 with 40 members signing the charter under the spiritual leadership of mission developer, Pastor Rudolf Johnson. Pastor Johnson had conducted the first church service nearly a year earlier at the community swimming pool in Park Village. The congregation also met at the El Dorado Hills Fire Station and later with their first pastor, Pastor Carl Schneider, at the then community center in Governors Village. Sunday School classes were held in private homes. In early 1965, the Pacific Southwest Synod of the American Lutheran Church purchased a parsonage in Park Village and 4.5 acres at the current site, and plans to begin construction of the church complex. The large cross at the front of the church was erected for dedication in March of that year.

Despite cutbacks in the aerospace industry, which affected community and church growth, the sanctuary was completed and dedicated in October 1968, with the leadership of Pastor John Olson. Church life began to grow and expand. The church sponsored the first community newsletter and formed a senior citizen group and the Newcomers' club. The church also opened its doors to organizations such as Alcoholics Anonymous, a cooperative preschool, Camp Fire Girls, and Girl Scouts. The church sponsored Boy Scout Troop 454 and continues sponsoring them today. The Greg Robinette Park, an Eagle Scout and God and Country Project, was completed with the help of scouts and members and friends of the church.

A period of sustained growth continued after Pastor Roger Lee came to St. Stephen's in 1971. The Youth Group was formed and the first youth was elected to the church council. The Lutheran Church Women, now called the Women's Group, was also organized. In 1976, during Pastor Dale Johnson's ministry, construction began on the Educational/Fellowship Hall. The Hall, built by church members, was completed and dedicated in October 1980 during Pastor Ken Peterson's tenure. The new building made it possible for the church to sponsor the St. Stephen's Day Care. (Today, Froggie Frontier Preschool continues that tradition under independent ownership). During the period, the congregation doubled in size and in 1984 became independent of support from the Board of American Missions.

Rapid growth continued during Pastor William Busch's service, beginning in 1985. Worship and Sunday School attendance increased and the sanctuary was expanded for additional seating. New pews were purchased to replace the first pews donated by St. John's from their original sanctuary. Donors to St. Stephen's have been many.

In 1994, Pastor Mark Winter was installed, and under his leadership there was a growth in membership to 500 plus members. Pastor Ron Hovick was installed in 2000.

Pastor Ron Rentner has served as pastor since January 2010. His experience includes leadership of large and small congregations, advocacy ministry, disaster response coordinator, affordable housing and service as a missionary in Guatemala.