Agesen has been hired after what Viborg called "a long and thorough process" and succeeds Jesper Fredberg, who joined RSC Anderlecht to become CEO Sports.
The 39-year-old had been Chief Scout at Danish Superliga rivals Randers since 2021.
Agesen played for the likes of AC Horsens and Randers before retiring in 2018.
He said: "It has been an ambition of mine to get to work in a role like this, and it is something I have been very curious about for several years, and have worked to improve my skills in that direction, so I am extremely looking forward to it to get started."
Director Morten Jensen added: "In Mads Agesen, we get a manager who comes with great football expertise, is a good communicator and has experience with both player recruitment and the use of data, where he will naturally have a key role in the collaboration with our scouting team and Football Radar [the data company that owns the club].
"At the same time, he is a team player who understands the value of a strong collective, and he comes from a club that is also used to fighting bigger budgets with success. We have identified a person who will both fit in well with us and who is very hungry to become part of VFF."
Viborg, Randers and the rest of the Danish Superliga have access to TransferRoom through a ground-breaking, league-wide agreement.
Fredberg will be appearing on a Super Users panel session at the TransferRoom Summit London on March 20. Register for this exclusive event here.
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