Early in the 20th Century, Klagetoh was served by priests from St. Michael and Keams Canyon. The Franciscan mission in Klagetoh was begun in 1924, with a church dedicated to St. Anne on June 5, 1927.

In 1961, the wide spread area served from Klagetoh became a parish. Fr. Francis Borgman, OFM, was named pastor and he set about building a rectory. At that time, Ganado and Greasewood became missions of Klagetoh. In 1983, a kitchen addition was built in the hogan social center to better serve the community needs. Klagetoh is much more remote than Ganado. The pastor was alone most of the time in Klagetoh. So that the pastor could have more visits from fellow priests as they traveled from Chinle or Keams Canyon to Gallup, the parish center was moved from Klagetoh to Ganado in 1986.