Head-to-head is a scoring system that counts wins and losses for individual team matchups, usually on a weekly basis. It's often very similar to the traditional format used in fantasy football.
Rather than using a cumulative scoring system in which teams accrue points in various statistical categories over the course of the season, head-to-head leagues pit one team against another in a win/loss format.
For instance, in a head-to-head league, Team 1 would match up against Team 2, and whichever team accrues the most fantasy points -- or wins the most categories -- over the course of a given time span is awarded the win.