A skill in Phantasy Star Online 2 is an ability specific to a class and selected from a skill tree.

A character can have up to two skill trees active, one from the character's main class, and one from the character's subclass. Skills from a subclass's tree function normally, except for rare mastery skills, which function only while the tree's class is the character's main class. Subclass skills pertaining to weapons do not grant the ability to equip those weapons, but still apply if a weapon of that type usable by the character's main class is equipped.

Each skill has from 1 to 10 levels available, and the character purchases each level by expending a skill point (SP). The total number of skill points a character can spend on a class's skill tree equals the number of levels the character has in that class, plus up to 10 skill points for that class earned from client orders. Most skills have a certain level in another skill as a prerequisite.