Seal Online is mostly a point-and-click MMORPG; movement, combat, and many other commands are all controlled by mouse, though the combo system is done with the A, S, and D keys. The player can choose from 7 different classes to start with. However, if the player chooses to start with the Beginner, he/she can choose to job change into the other 6 classes when he reaches Level 10. 21 additional new classes were added in early 2009. The game experienced a wipe on 27 September 2010 bringing all players back to level 1.

Seal Online's travel system uses a method called 'Warp Gates'. These gates, located in various towns, allow the player to move to other maps. Players may use scrolls, set revive points, use the Wagon Driver NPC, or just type out a Teleport command for a small fee to warp to different maps.

Players can learn skills to trade, open or join a guild after completing a quest, open a chat room, create a party to fight monsters more effectively, open an in-game bank account to hold or collect more items and money, nurture a pet, do quests, and fish.

Seal Online's level up system uses a point method. Skills level up with skill points. Each time a player levels up, they receive a set number of skill points and status points, which they then may use to strengthen their character.

The Combo System is more complicated than most other MMORPGs. As a player attacks an enemy, the XP bar fills up. Once the bar is halfway filled, the player can start a combo by pressing the game's combo buttons. After starting a combo, players must press a combination of buttons. Combos do more damage than normal attacks, and are executed faster.