Waggoner (January 12, 1855 – May 28, 1916) was a Seventh-day Adventist particularly known for his impact on the theology of the church, along with friend and associate Alonzo T. Jones at the 1888 Minneapolis General Conference Session.

At the meeting of the General Conference of Seventh-day Adventists Ellet J. Waggoner along with Alonzo T. Jones presented a message on justification supported by Ellen G. White, but resisted by church leaders such as G. I. Butler and others.

In 1883, Waggoner stopped practicing medicine and became the assistant editor for the Signs of the Times – an official paper presenting the stands and views of the Seventh-day Adventist Church.

In 1888 Waggoner presented his ideas regarding righteousness by faith at the General Conference session held in Minneapolis, Minnesota.

He remained there for ten years, working with W. W. Prescott in the training school in England, and continuing in his writing and studies on Christ and His righteousness.