As the second principal of Bannock Academy, Charles Nephi Watkins strove to uphold the standards set by Jacob Spori, and to continue to build the school. He was called to the position in 1891, when the Academy was still relatively new and struggling financially. Local Church members were asked to make financial contributions to help keep the school in operation. Since there was only one other teacher in the Academy at the time, Principal Watkins was involved in teaching full-time in addition to his administrative role.
Watkins continued to teach at the Academy until 1896, even though health reasons had caused him to resign from his position as principal in 1894.