Sextus was the son of Gnaeus Pompeius but his mother is unknown. The date and place of his birth have not been found.
His wife was Lucilia. They were married, but the date and place have not been found. Their three known children were Pompeia (?-?), Sextus Pompeius Virdoctus (?-?) and Gnaeus Pompeius Strabo (?-0087BC).