A presidential order published on Monday announced the appointment of Major General Anatoliy Barhylevych as the new commander.
A separate order announced the removal of General Ihor Tantsyura, who had been in the post since May 2022.
No reason was given for the decisions.
Barhylevych, 54, had since last year been serving as chief of staff of troops in eastern Ukraine, where fighting has been heavy since Russia sent in tens of thousands of soldiers in February 2022.
Part of the armed forces, the Territorial Defence Forces' roles include protection of critical facilities, combating sabotage and enemy intelligence forces as well as maintaining security in Ukraine.
They are also primarily responsible for organising defences away from the front lines.
The Territorial Defence Forces grew out of volunteer reserve groups during fighting in eastern Ukraine that began in 2014, and have since been reorganised several times.
Barhylevych was involved with building up the forces.
Zelenskiy named a new defence minister, Rustem Umerov, last month.
Umerov has said his priorities include making the ministry the main institution for co-ordinating Ukrainian defence forces, enhancing the value attached to individual soldiers, developing Ukraine's military industry and fighting corruption.
with DPA
