PvP in Star Trek Online will be surprisingly important, because of the importance that it holds for the Klingon faction. Different from the Federation Starfleet, the Klingon faction is highly dependent on PvP for player progression. Basically, the more enemies defeated in PvP the more skill points obtained and the higher rank you can achieve. Players of Star Trek Online will have a choice of battling out among the same faction or a different faction, or battle it out yourself or team up to defeat other Star Trek Online gamers.

The topic about the imbalance of the Klingon faction and the Federation faction is a hot topic that the Star Trek Online community are rather displeased, Cryptic Studios claim that although it is a featured added very late in the development, but as the game progresses over time, new updated contents will eventually sort out the imbalance or other irregularities in the game.