Portal Fighter II features several modes. First, there are story modes for each character, in which players must fight their way through a long series of opponents, with each fight being best out of three rounds. Second, there is a Survival mode, in which players fight as many rounds as possible without having their health bar restored. There are also 1 Player and 2 Player modes, in which the player can have a single fight against either the computer or another player using the same keyboard.
In total, the games has twelve initial characters, six unlockable characters, thirteen initial stages, and three unlockable stages.
With the exception of Survival mode, all fights consist of three rounds, unless one fighter manages to win the first two rounds. A round is won by attacking an enemy until their health bar is eliminated. Fights have time limits ranging from 20 to 99 seconds, which can be changed from the main menu. However, the default 40 seconds is longer than most fights last, usually making time a nonissue. On the rare occasion when time does run out, the combatant with more health remaining wins. The difficulty can be changed from the main menu.
The player navigates the game's menus using the mouse, but fights using the WASD keys. The A key is used to dodge, the S key can be used to execute a slower, more powerful attack, and the D key executes a quicker, weaker attack. As the player fights, a special gauge is filled, which ultimately allows the player to enact their character's special attack with the W key. The second player fights using the arrow keys, which function the same way as their counterparts.
Portal Fighter II combines a fairly crude bold outline style with the original style of the various characters and stages. Stages corresponding to series use the native soundtracks. The main theme of the game is the Endless Handbag Loop.
Although not as popular as its spiritual sequel, Newgrounds Rumble, Portal Fighter II was a smash hit of a game, with over 1.2 million views as of December 2010. Despite only having a fairly typical score and a good but unremarkable average review of 8.5/10, the game is featured in three collections: Fighting Games, the Flash Portal History, and Newgrounds parodies. The game also won a Daily Feature.