The Secretariat acts as main reference and service point for the Parties to the Carpathian Convention. It supports the work of the different bodies of the Convention, is responsible for the coordination of the Programme of Work of the Convention and assists in project development and implementation.

Furthermore, the Secretariat facilitates research, communication and information exchange on matters related to the Convention and prepares reports on the Convention for the COP. It represents the organization in external relations and coordinates its activities with other international bodies.

Article 15 of the Carpathian Convention provides the legal basis for the establishment and the concrete functions of the Secretariat.

Since 2004, the Secretariat has been provided by UN Environment through its Office in Vienna (until 2014 "ad interim"). The Secretariat is also assisted by the European Academy (EURAC) through the EURAC Representing Office in Vienna.

The Secretariat is headed by Mr. Harald Egerer.