c. 1400, "withdrawal, removal," from Late Latin subtractionem (nominative subtractio) "a drawing back, taking away," from past participle stem of Latin subtrahere "take away, draw off, draw from below," from sub "from under" (see sub-) + trahere "to pull, draw" (see tract (n.1)). The mathematical sense is attested from early 15c.
Þou most know þat subtraccion is drawynge of one nowmber oute of anoþer nomber. ["The Crafte of Nombrynge," c. 1425]