Wordorigins.org

The word pill ultimately comes from the Latin pila “ball,” or more specifically from the Medieval Latin pilula “little ball.” So a pill is a small ball or pellet of medicine. This is the earliest sense of the word in English, dating to before 1400, appearing in the English translation of Lanfranc’s Science of Cirurgie in Bodleian Ashmole MS 1396:

He schal ofte be purgid wiþ pillis cochie rasis.