There are many more skills available in Lemmings 2: 51 in total (although no more than eight are available in each level), as compared to eight in the original game. Some of the skills are similar to the original ones (like digging and building variants), while others are all new (several flying skills, for example). One skill, the "attractor", will cause the lemming to play a musical instrument and have nearby lemmings stop walking to do a dance. The instrument and dances performed vary by tribe.

A practice mode was also added. In this mode, any type of skill available can be selected for the player to experiment with. There is a choice of four different practice levels. There is still a total of 120 levels, but in this game they are divided into ten levels for each of twelve tribes. Each tribe's levels can be started at any time, and progress can be saved from the main menu. The player starts out with 60 lemmings for each tribe, but only one lemming needs to make it to an exit in order to progress to next level. The number saved will then be the number left in the next level. As some levels may require several lemmings to complete, the player might have to replay an earlier level to save more lemmings for the following ones if they realize they do not have enough.

The player will be rewarded with a bronze, silver or gold medal, depending on how many lemmings are saved in the level. This will also dictate the type of the talisman part received once all the tribe's levels are completed. To watch the outro and credits, all golden talisman parts need to be won by rescuing enough lemmings from each tribe. A new fast forward button and fan button have been added to the controls. The fast forward replaces the release rate button in the original game, which would let the player release more lemmings at a time. The fan button turns the cursor into a fan, which is used to push around any flying lemmings or to affect wind-powered elements.