http://tvline.com/2015/11/24/supergirl-casting-superman-season-1-episode-13-kal-el/

CW is seeking a 13-year-old actor with “future leading man looks” to play the young Kal-El, according to TV Line. He’ll first appear in the season’s 13th episode.

it still could be just a flashback episode - it doesn't necessarily mean that she will interact with him at all.