The High Court of Justice is divided into the following divisions: Civil, Criminal, Contentious-Administrative and Labour Divisions

Its functional structure consists in a Chief Justice who is also the Chief Justice of the Civil and Criminal Divisions and will have the rank of a Supreme Court Justice while in office, of the Division Chief Justices and Judges established by law for each division and where applicable, of the Sections into which each Division may divided.

The president of the high court of Navarra represents the judiciary in the autonomous community. The president is appointed by the General Council of the Judiciary for a term of five years.  The president of the high court combines govermental and representative tasks of the post with the jurisdictional duties of president of the civil and criminal court of the high court.   

Magistrate Juan Manuel Fernández Martínez has presided over the high court of Navarre since February 2004, having been re-elected for a new term of office by the General Council of the Judiciary in February 2009.