Reflecting its nautical heritage, the term captain is used as a military title by officers of more junior rank who command a commissioned vessel of the Navy, Coast Guard, or National Oceanic and Atmospheric Administration (NOAA) of patrol boat size or greater.

Promotion to captain is governed by Department of Defense policies derived from the Defense Officer Personnel Management Act (DOPMA) of 1980 or its companion Reserve Officer Personnel Management Act (ROPMA).

DOPMA/ROPMA guidelines suggest that no more than 50% of eligible commanders should be promoted to captain after serving a minimum of three years at their present rank and after attaining 21–23 years of cumulative commissioned service, although this percentage may be appreciably less, contingent on force structure and the needs of the service.

A smaller cohort outside of sea and shore commands may also serve as astronauts on loan to the National Aeronautics and Space Administration (NASA).

In contrast, commanders of aircraft carrier strike groups (CSG) and expeditionary strike groups (ESG) are normally rear admirals, while subordinate destroyer squadron commodores, amphibious squadron commodores, carrier air wing commanders and the individual ship commanding officers within the strike group are of captain rank or lower.

Adding to the confusion, all commanding officers of commissioned U.S. Navy warships and submarines (e.g., USS or "United States Ship") are called "captain" regardless of actual rank.

Coast Guard captains follow career paths very similar to their Navy counterparts, with marine safety, security, and boat forces officers serving as Captain of the Port in command of Coast Guard Sectors, seagoing officers typically commanding large maritime security cutters or high endurance cutters and aviators commanding Coast Guard air stations.