The designation Caritas Czech Republic is used in a broader sense to describe the whole charity network, and in a narrower sense for the part formally called the Caritas Czech Republic Secretariat, which is based in Prague and coordinates charity activities at the national level. The Secretary-General for the Caritas Czech Republic is Jakub Líčka.

In addition to coordinating the work of the individual Caritas, the Caritas Czech Republic Secretariat organizes national collections, including the Three Kings Charity Collection, convenes expert collegium, cooperates with foreign organizations Caritas Internationalis and Caritas Europa and runs a hotel and training centre Marianeum in Prague.

The Secretariat Caritas Czech Republic comprises the Humanitarian Aid and Development Cooperation Department, the Expert Agendas Department, the Fundraising and Communications Department and the Economics Department.