SUNY Maritime offers Master of Science degrees in International Transportation Management and Maritime and Naval Studies. Both programs offer students the opportunity to earn a U.S. Coast Guard Merchant Mariner deck officer license, which qualifies them to operate marine vessels, in addition to their degree.

The college offers a stand-alone Advanced Certificate in Supply Chain Management and a certification in International Ship Chartering. Both certificates may be earned on their own, or in conjunction with the International Transportation Management master's degree program.