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," 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]