Alden has held the post since 1998. During his tenure the school has expanded its athletic budget and facilities, and Alden also oversaw the Missouri's move from the Big 12 to the SEC prior to the 2012-2013 school year.
In a statement released Thursday afternoon, Alden said that the change was a personal decision.
"After several months of reflection, I've decided it is time for a change, both for me and for the University that I so dearly love," Alden said in a letter. "My wife, Rockie, our son, Jake, and I have had an incredible experience at Mizzou and this is simply our next step in our journey in Columbia."
While Alden will leave his position with the athletic department, he will not depart the university. According to Morrison, Alden will take a position with the school's College of Education, in which he will take part in the school's Positive Coaching Program as well as higher education leadership courses.
Alden has said that the College of Education, working with other partners on campus, would launch a Center for Global Service Learning Leadership.
Alden, a native of Illinois, hired Gary Pinkel, then the coach at Toledo, to helm the Tigers' football team in 2001. Pinkel has since become the school's winningest coach and taken the team to two consecutive SEC East titles.
The school plans to hold a press conference on Friday to discuss Alden's AD departure and new role.