Clinical protocol, has a more specific meaning. It describes a method to be used in a clinical trial (e.g. of a drug or medical treatment) or a medical research study.
A set of rules followed by providers such as EMTs or nurses. Often considered to be stricter than a guideline, and to carry more weight with the law, but there is no hard evidence to support this view and the terms are usually used interchangeably.
see Stupp protocol.