'synapsida' originates from New Latin (taxonomic usage), ultimately formed from Greek roots: 'syn-' meaning 'together' and 'apsis' (or a related form) meaning 'arch' or 'arch-like structure', used in reference to the skull configuration.

'synapsida' was coined in modern (19th–20th century) scientific Latin as a taxonomic name based on Greek elements; the New Latin form 'Synapsida' became established in vertebrate paleontology to denote the group now known by that name.

Initially formed as a descriptive taxonomic term referring to a particular skull feature ('together/arch'), it has come to denote the clade of amniotes (the mammal lineage and its relatives) rather than only the anatomical feature.