Flea-bane, the odour being, as it is supposed, hateful to fleas This is a real curiosity of blundering derivation. The Latin word is pulecium, the flea destroyer, from pulex, a flea, softened into pulegium, and corrupted into the English-Latin pule'-regium. “Pule,” changed first into puny, then into penny, gives us “penny-regium,” whence “penny-royal.” The French call the herb pouliot, from pou (a louse or flea).
Source: Dictionary of Phrase and Fable, E. Cobham Brewer, 1894
More on Pennyroyal from Infoplease: