鞭毛虫（英语：Flagellate），指身上具备一根或多根鞭毛的微生物。在动物组织中，也有类似鞭毛虫的细胞，如精虫。它通常被用来当作具备鞭毛器官的原生动物的统称。

A flagellate is a cell or organism with one or more whip-like organelles called flagella. The word flagellate also describes a particular construction (or level of organization) characteristic of many protists (eukaryotic organisms) and their means of motion. The term presently does not imply any specific relationship or classification of the organisms that possess flagellae. However, the term "flagellate" is included in other terms (such as "dinoflagellate" and "choanoflagellata") which are more formally characterized.