Keio Flying Squadron 2 was released in 1996 for the Sega Saturn in Japan, Europe, and Australia. The second installment of the series continues the story of Rami's adventures as the Keeper of the Secret Treasure (a sphere passed down through generations of Rami's family). Rami races Dr. Pon and a new rival Himiko Yamatai for an ancient treasure that can be unlocked with six spheres. Two of the stages retain the shoot-'em-up style of the first game, but the lesser dragons can be obtained as bonuses only.

Mainly the stages consist of sidescroling platformer stages. These scroll from right to left on the Japanese version and left to right on all other versions. Several bonuses can be collected including three weapons (Rami can also bounce on the heads of enemies to defeat them):

A large mallet, used only for hitting enemies

An umbrella, used to hit enemies, float and deflect overhead obstacles

A bow, used to shoot arrows at enemies.

Besides the platformer and shoot-'em-up stages, there is vertically scrolling special stages, an underwater stage and a rollercoaster stage, making the game a multi-genre platformer. Points spheres can be collected throughout the game. A reward system accessed from the main menu unlocked helpful hints and behind-the-scenes extras depending on the highest and lowest scores achieved through playing.