CARNet operation is realised through a series of interconnected services (permanent tasks) and projects (tasks of limited duration, oriented towards establishing of new services and improvement of the existing ones). Basic organisational units are project teams and task groups.

Departments operating within CARNet are:

• Network Infrastructure Department
• Computer and IT Systems and Services Department
• Computer Security Department
• National CERT Department
• User Support Department
• Education Support Department
• General and Financial Activities Department
• Office of the CEO

Managing Council represents the interests of CARNet founders, the Croatian Government. The Managing Council members are appointed by the Minister of Science and Technology. Since 12 July 2011 the members of the Managing Council are:

• Ivan Marić (Chairman of the Board)
• Mladen Mustač
• Ružica Vučić
• Dario Mikić
• Barbara Kolarek

CARNet Executive Committee co-ordinates short- and long-term planning, and makes decisions on business organisation and is responsible for the relations with the government bodies, users, partners and the public, and its members are:

• CEO (Zvonimir Stanić)
• Vice CEO (Vlado Pribolšan),
• Deputies CEO (Nataša Glavor, Ivana Golub, Marijana Pezelj, Andrijana Prskalo Maček, Radovan Kovačević, Darko Perhoč, Branko Radojević).

The Users Board is CARNet advisory body formed by all CARNet co-ordinators at member institutions. Since 14 July 2005 the President of the CARNet Users Board is Damir Mrkonjić.