The basic independent unit is the local church.  They do not, however, function in isolation.  The Czech Baptist Union is a community of Baptist churches within the Czech Republic, which voluntarily associate in agreement in the areas of work in which they will cooperate. The highest council of the Czech Baptist Union is the congress of delegates, which meet, as a rule, once a year.  Between the meetings of the congress, the council of church representatives takes place.  The administrative authority is the administrative committee, which has five members that are elected in by the congress for four-year terms.  The congress also votes on the revision committee.  The office of administration takes care of the daily affairs of the Czech Baptist Union.

The Czech Baptist Union is a member of the European Baptist Federation and the International Baptist Union.  These organizations help with the exchanging of information and cooperation, but they are not a superior authority.

The education of workers is insured in various ways.  A thematic conference takes place every year and all the members of the churches and any other interested people are invited to attend.  A long-distance theological seminary is used for the education of laymen, preachers, Sunday school teachers, and other church workers.  A higher specialty school of social work and theology, Dorkas in Olomouc, gives three years of specialty study in the branches of social work and theology. To be accepted for study, a prospective student must show his faith by his lifestyle, have evidence of a personal relationship with Jesus Christ, have relevant motivation for study, and fulfill the conditions set by the government for this type of study.  The school is open for many denominations of Christians.  Those who want to study theology and are in the Czech Baptist Union also study in Prague at the Evangelical Theological Seminary or at the Evangelical Theological College at Charles University.  They may also receive further education from seminaries abroad and so on.