WNYMCS’s mission is to develop cadets in mind, body and character, to prepare them for further education, and to prepare them to be effective leaders and responsible citizens.  There are four cornerstones to this mission – Academic Excellence, Character Development, Physical Development, and Leadership Development.

The mission statement of Western New York Maritime Charter School calls leadership and character development the inherent cornerstones of the school. Faculty and staff lead by example in all facets of campus life, following the time-honored tradition of military and maritime courtesy, and use of the Chain of Command. The Chain of Command, modeled on that in the military consists of an unbroken leadership chain of individuals from the student's teacher through the Commandant, to the President of the Board of the Trustees. Extending through all levels of leadership, the Chain of Command is a two way communications channel, conveying information, support and assistance. Policy is set and instructions are given, and outcomes, results , and information are shared. Leadership is taught and reinforced all through the Chain of Command. These individuals model appropriate behavior in appearance, actions, and attitudes. They demonstrate honor, integrity, and respect for the dignity of all members of the school community. They practice self-discipline, control in school, and students learn from their example. Students are expected to follow these examples, rejecting any behavior by themselves of their fellow students that does not rise to the standards of the school community. Faculty, staff, and students have certain rights and responsibilities, summarizing in the Code of Conduct. Students who choose to become part of this school community choose to abide by the Code of Conduct.