Using your Flagellants to guard one flank (usually the weaker flank) of your battle line is a tried-and-true Empire tactic. Often, the presence of the Flagellants alone is enough to deter your enemy from attacking your weak flank. This deterrent allows you to use your hardest units offensively, because you don't have to hold anyone back to guard your flank.

Instead of guarding your flanks (or perhaps as they guard your flanks), Flagellants can protect your valuable and vulnerable artillery and missile troops. If you're fortunate enough to have a hill or other defensible area conducive to missile fire in or near your Deployment Zone and a large number of missile units and/or artillery pieces, it's certainly a good idea to concentrate your missile power in that area and use your Flagellants as guards. However, a large unit of Flagellants is wasted guarding a single war machine or unit of Crossbowmen, Archers, or Handgunners. Generally, use your Flagellants for this type of guard duty only when the missile troops and artillery cost more points than the Flagellants guarding them.

You can use your Flagellants to guard, take, or prevent the enemy from obtaining scenario objectives. For instance, if you're playing the Capture scenario from the Warhammer rulebook and the objective is a bridge in the centre of the table, park your unit of Flagellants on the bridge. Even better, park your Flagellants on the enemy's side of the bridge and manoeuvre another strong unit onto the bridge itself. That way, even if the last Flagellant falls toward the end of the game, your second unit can still claim or contest the objective. Variations on this tactic can also be used in other types of scenarios. For instance, in the Breakthrough scenario, a large unit of Flagellants deployed in a single rank could cut off access to a large section of your deployment zone and thus prevent your opponent from fulfilling his mission objectives. Similarly, in a siege game, a unit of Flagellants deployed in front of a castle gate will require any unit armed with a log or battering ram to fight a long and bloody battle before it even begins to assail your castle's gate.

Beware of flyers when using your Flagellants as guards. Flyers can easily swoop around your guards and attack the troops or objectives behind. If you've committed your Flagellants to guard duty and your opponent has a powerful flyer or unit of flyers, make sure that you destroy or neutralise it. Otherwise, you'll have given your expensive Flagellants a mission they cannot fulfill and wasted them in the process.