Following Smith's resignation last year, Nye remained as a deputy to state Superintendent Sydnee Dickson.
"He will be greatly missed," Dickson said in a statement. "But we celebrate with him in this new opportunity to improve outcomes for students in Ogden School District."
Nye is expected to remain in his current position until June; his successor as deputy state superintendent has not yet been named.
In a statement, Nye said he had hoped to return to Ogden after leaving the district in 2015. He said two years with the Utah Board of Education had given him a better understanding of statewide education policy.
Ogden School District enrolls roughly 12,000 students, according to the latest enrollment data from the Utah Board of Education. It is one of three districts in which most students are not white, and the only majority-Hispanic school district in Utah.
"What an honor and privilege," Nye said. "I am truly humbled and am inspired by the dedication of the administrators, teachers, and students [to] the well-being of our district and community."
State school board Chairman Mark Huntsman praised Nye's contributions to the state's public education system.
"Dr. Nye's leadership has been critical in helping to build a strong administrative team at the state [school] board," Huntsman said. "That team will continue to build upon many of the positive changes he has influenced over the last two years."
Nye's career in education includes experience as a classroom teacher as well as administrative roles at the school, district and statewide levels. He holds two master's degrees, from Arizona State University and Weber State University, as well as a doctorate from Utah State University.