Board Thread:Battle Nations Discussion/@comment-12.238.87.162-20140808183547/@comment-11090687-20140808192205

They drop 100% (3 Skulls) from Raider encounters with one of the Raider Luitenants (Sarin, Tronk, Crazy Blades). These encounters only spawn on outposts of players in the level range Lvl.30-Lvl.50, so check the outposts of in-game friends you have that are in this level range. Kill the encounters with the Sarin/Tronk/Blades icon.

Other ways of getting skulls are through Boss Strike rewards and the things Bobmath mentioned above.