Head is often a part of a title of office, meaning "the highest". A "head of department" is thus the person with the highest standing in said department. This use might stem from the fact that the head is the highest placed part of the human body, or from the fact that the brain and therefore cognitive functions and decition making is located in the head.
Some dictionaries define close to thirty meanings to the word. However, most of the usages are associated with the connotation of forward, top, essential, control etc. which are derived from attributes of an animal head (or brain). Perhaps the only exception is the latrine of a marine vessel which is also called the head.