'contra-peduncular' is formed from the Latin prefix 'contra-' meaning 'against, opposite' and Neo-Latin/Latin 'pedunculus' (from which English 'peduncle' derives) meaning 'little foot, stalk-like projection'.

The element 'peduncle' comes into English via Medieval/Neo-Latin 'pedunculus' meaning 'small foot' or 'stalk'; the prefix 'contra-' (Latin) has long been used in scientific and medical formations. The compound usage (often hyphenated) arose in specialist anatomical and botanical descriptions as 'contra-' + 'peduncular' to denote position opposite the peduncle.

Initially constructed to mean 'opposite the peduncle' in technical descriptions; this locational sense has remained stable and is specialized to anatomical/botanical usage.